4.7.2

Switches the recommended primary tool for version control operations from
raw `git` commands to using `but` (GitButler CLI). This change ensures
that all write operations, such as committing, are standardized and
executed through the dedicated CLI. Read-only inspection via standard
`git` remains allowed.

AGENTS.md

@@ -0,0 +1,8 @@
+# Agent Instructions
+
+## Version Control
+
+- Use `but` (GitButler CLI) for version-control operations in this repository.
+- Use `but` for all version-control write operations; read-only `git` inspection is allowed.
+- Do not access GitHub URLs directly. Use the `gh` CLI for GitHub operations.
+- When committing, use English Conventional Commit messages and include a clear description of Why and What.

CLAUDE.md

@@ -17,4 +17,12 @@
 - Component organization: Feature-based folders with __tests__ subdirectories
 - Testing: Describe/it blocks with clear test descriptions
 - Async/await for asynchronous operations
-- Modular architecture following Obsidian plugin patterns
+- Modular architecture following Obsidian plugin patterns
+
+## Architecture: Settings Flow
+Settings flow through 3 layers. When adding a new setting, all 3 must be updated:
+1. `src/settings/settings-info.ts` — `AutomaticLinkerSettings` type + `DEFAULT_SETTINGS`
+2. `src/replace-links/replace-links.ts` — `ReplaceLinksSettings` interface
+3. `src/main.ts` — Two call sites that bridge (1) to (2): `modifyLinks()` and the selection command
+
+When adding a field to an interface, always grep for all sites that construct objects of that type to ensure the new field is passed through.

PLAN_AI_DISAMBIGUATION.md

@@ -0,0 +1,56 @@
+# プラン: Gemma 4 による「あいまいさ解消（Disambiguation）」機能の実装 (2-Pass 方式)
+
+このプランは、Obsidian Automatic Linker において、Gemma 4 (Local LLM / LM Studio) を用いて文脈に最適なリンク先を選択、および既存の誤ったリンクを修正する機能を導入するものです。
+
+## 1. 現状の分析と課題
+- **データ構造の制限**: `src/trie.ts` の `CandidateData` インターフェースが単一の `canonical` パスしか保持できない。
+- **重複登録の挙動**: `buildCandidateTrie` 関数において、同じ名前の単語やエイリアスが見つかった場合、最初に見つかったものが優先されるか、後から来たもので上書きされている。
+- **既存リンクの誤り**: 機械的な処理や手動で作成された不適切な `[[Note]]` リンクの存在。
+- **パフォーマンス**: AI 処理は低速なため、コマンドによる明示的な実行と、進捗バー付きの UI フィードバックが必要。
+
+## 2. 実装フェーズ
+
+### フェーズ 1: データ構造の拡張 (Data Structure)
+- [x] `CandidateData` インターフェースの修正 (`src/trie.ts`)
+  - `canonical`, `scoped`, `namespace` を持つオブジェクトの配列を保持できるように変更。
+- [x] `buildCandidateTrie` の修正
+  - 重複する名前やエイリアスがある場合、既存の候補リストに `push` するように変更。
+- [x] **完了条件**:
+  - `src/trie.ts` の既存テストおよび新規追加テスト（複数候補の保持）がパスすること。
+  - `pnpm lint` および `pnpm tsc` (タイプチェック) でエラーがないこと。
+
+### フェーズ 2: AI 連携クライアントと「解決ロジック」の実装 (AI Integration)
+- [x] `src/utils/ai-client.ts` の新規作成
+  - OpenAI 互換 API へのリクエスト処理とプロンプト設計。
+- [x] 非同期スキャン関数 `resolveAmbiguities` の実装
+  - 1. 新規リンク候補（複数候補あり）の特定。
+  - 2. 既存リンクの再検証（別のより良い候補がないか）の特定。
+- [x] **完了条件**:
+  - モックを使用した `resolveAmbiguities` のテストがパスすること。
+  - `pnpm lint` および `pnpm tsc` でエラーがないこと。
+
+### フェーズ 3: リンク置換エンジンの拡張 (Sync Logic Enhancement)
+- [x] `src/replace-links/replace-links.ts` の `replaceLinks` 引数の拡張
+  - `resolvedAmbiguities?: Map<string, string>` を受け取り、優先的に適用する。
+- [x] 既存リンクの「張り替え」ロジックの追加。
+- [x] **完了条件**:
+  - `replace-links.test.ts` に AI 解決マップを使用したテストケースを追加し、パスすること。
+  - `pnpm lint` および `pnpm tsc` でエラーがないこと。
+
+### フェーズ 4: UI 実装とコマンドの追加 (UI & Integration)
+- [x] `Automatic Linker: Run AI Link Enhancer` コマンドの実装。
+- [x] 進捗バー付き `Notice` による UI フィードバックの実装。
+- [x] `src/settings/settings.ts` への AI 設定追加。
+- [x] **完了条件**:
+  - Obsidian 上での実機動作確認（Notice の表示、リンクの修正・生成）。
+  - 全体のビルド (`pnpm build`) が成功すること。
+
+## 3. 共通の品質基準 (Definition of Done)
+- 各フェーズの最後には必ず以下のコマンドを実行し、エラーがないことを確認する。
+  1. `pnpm test` (または `vitest`)
+  2. `pnpm lint`
+  3. `pnpm tsc`
+
+## 4. リスクと対策
+- **エディタの不整合**: AI 処理開始時のテキストのスナップショットを保持し、置換時に大幅な変更があれば警告を出す。
+- **トークン制限**: 段落単位での分割処理により、長いノートにも対応。

README.md

@@ -33,13 +33,22 @@ The plugin automatically detects file names in your text and converts them to wi
 - **CJK Support**: Full support for Japanese, Chinese, Korean, and other CJK languages
 - **Case Sensitivity**: Optional case-insensitive matching
 
+### AI Link Enhancer (Beta)
+
+Resolve ambiguous links and correct existing ones using AI:
+
+- **Disambiguation**: When multiple notes have the same name or alias, the AI selects the most appropriate one based on context.
+- **Link Correction**: Automatically verify and correct existing wiki links if a better candidate is found.
+- **Local LLM Support**: Connect to any OpenAI-compatible local AI server (e.g., LM Studio, Ollama).
+- **Context-Aware**: Uses surrounding text to provide the AI with necessary context for accurate linking.
+
 ### Smart Namespace Management
 
 Organize large vaults with sophisticated namespace handling:
 
-- **Base Directory**: Define a base directory (e.g., `pages/`) where the prefix is omitted from links
+- **Base Directory**: Use Obsidian's "Folder to create new notes in" setting as the base directory where folder prefixes are omitted from links
 - **Proximity-based Linking**: Automatically resolve shorthand links to their full namespaced paths
-- **Namespace Restriction**: Use `automatic-linker-scoped: true` in frontmatter to restrict linking to files within the same namespace
+- **Namespace Scope**: Use `automatic-linker-scoped: true` in frontmatter to restrict linking to files within the same namespace
 - **Closest Match Selection**: When multiple candidates exist, the plugin selects the file closest to your current note
 
 ### URL Formatting
@@ -81,47 +90,58 @@ Access these commands via the Command Palette (Cmd/Ctrl + P):
 | **Automatic Linker: Format file** | Convert text to links in the current file |
 | **Automatic Linker: Format selection** | Convert only selected text to links |
 | **Automatic Linker: Format vault** | Batch process all files in your vault |
+| **Automatic Linker: Run AI Link Enhancer** | Use AI to resolve ambiguous links in the current file |
 | **Automatic Linker: Copy file without links** | Copy current file content with links as plain text |
 | **Automatic Linker: Copy selection without links** | Copy selected lines with minimal indent and links removed |
 | **Automatic Linker: Rebuild index** | Rebuild the file index for link candidates |
 
 ## Configuration
 
-### General Settings
+### Formatting Workflow
 
-- **Format on Save**: Enable automatic linking when saving files
-- **Format Delay**: Delay in milliseconds before formatting (useful for plugin integration)
-- **Base Directory**: Root directory for namespace handling (e.g., `pages`)
+- **Format on save**: Automatically format links when saving files.
+- **Format delay (ms)**: Delay formatting and post-format integrations by the configured number of milliseconds.
+- **Run Prettier after formatting**: Run the Prettier plugin after Automatic Linker formatting.
+- **Run Obsidian Linter after formatting**: Run Obsidian Linter after Automatic Linker formatting.
 
 ### Link Behavior
 
-- **Consider Aliases**: Include frontmatter aliases when matching text
-- **Proximity-based Linking**: Automatically resolve shorthand to full namespaced links
-- **Ignore Case**: Enable case-insensitive link matching
-- **Prevent Self-Linking**: Don't create links from a file to itself
-- **Ignore Date Formats**: Skip date-formatted text like `2025-02-10`
+- **Respect 'Folder to create new notes in' setting**: Use Obsidian's new-note folder as the base directory when omitting folder prefixes from links.
+- **Proximity-based linking**: Resolve shorthand links to the candidate with the most path segments in common with the current file.
+- **Include aliases**: Include frontmatter aliases when matching text.
+- **Remove aliases in directories**: Remove displayed link aliases for links targeting the configured directories.
+- **Ignore case**: Match links without requiring the same letter case.
+- **Match sentence case**: When Ignore case is disabled, match text capitalized only because it starts a sentence.
+
+### Exclusions
+
+- **Prevent self-linking**: Do not link text to the current file.
+- **Ignore date formats**: Skip date-formatted text such as `2025-02-10`.
+- **Ignore headings**: Do not add links inside Markdown headings.
+- **Ignore Markdown tables**: Do not add links inside Markdown table rows.
+- **Exclude directories from automatic linking**: Skip files in the configured directories when building automatic links.
 
 ### URL Formatting
 
-- **Format GitHub URLs**: Convert GitHub links to readable format
-- **GitHub Enterprise URLs**: Add custom GitHub Enterprise domains
-- **Format Jira URLs**: Convert Jira issue links
-- **Jira URLs**: Configure Jira domain(s)
-- **Format Linear URLs**: Convert Linear issue links
+- **Format GitHub URLs on save**: Convert GitHub URLs to readable issue and pull-request links.
+- **GitHub Enterprise URLs**: Add custom GitHub Enterprise domains.
+- **Format JIRA URLs on save**: Convert JIRA issue URLs to readable links.
+- **JIRA URLs**: Add custom JIRA domains.
+- **Format Linear URLs on save**: Convert Linear issue URLs to readable links.
+- **Replace URL with title**: Replace bare URLs with Markdown links using fetched page titles.
+- **Ignore domains**: Exclude configured domains from URL title replacement.
 
-### Advanced Options
+### AI Link Enhancement (Beta)
 
-- **Replace URLs with Titles**: Automatically fetch page titles for bare URLs
-- **Ignored Domains**: Exclude specific domains from URL title replacement
-- **Exclude Directories**: List of directories to skip during auto-linking
-- **Remove Alias in Directories**: Strip aliases from links in specified folders
+- **Enable AI Link Enhancement**: Add a command that uses a local LLM to resolve and correct ambiguous links.
+- **AI API Endpoint**: Set the URL of the OpenAI-compatible local AI server.
+- **AI Model**: Set the model name sent to the local AI server.
+- **Max Context Length**: Set the number of surrounding characters sent for each ambiguous link.
 
-### Integration
+### Diagnostics
 
-- **Run Obsidian Linter After Formatting**: Chain with Obsidian Linter plugin
-- **Run Prettier After Formatting**: Chain with Prettier plugin
-- **Show Load Notice**: Display notifications when files are loaded
-- **Debug Mode**: Enable verbose logging
+- **Show load notice**: Display a notice after the plugin loads Markdown files into its index.
+- **Debug mode**: Log debug information to the developer console.
 
 ## Usage Examples
 
@@ -141,7 +161,7 @@ I'm learning [[Python]] and [[JavaScript]] for web development.
 
 ### Example 2: Proximity-based Linking
 
-With `baseDir: "pages"` and Proximity-based Linking enabled:
+With Obsidian's "Folder to create new notes in" set to `pages/` and "Respect 'Folder to create new notes in' setting" enabled, along with Proximity-based Linking enabled:
 
 File structure:
 ```
@@ -159,7 +179,7 @@ When you type: `React uses TypeScript`
 
 It becomes: `[[frameworks/React]] uses [[languages/TypeScript]]`
 
-### Example 3: Proximity-based Linking
+### Example 3: Namespace Scope
 
 File `pages/team-a/internal.md` has frontmatter:
 ```yaml
@@ -237,6 +257,9 @@ automatic-linker-exclude: true
 # Restrict linking to same namespace only
 automatic-linker-scoped: true
 
+# Disable URL title fetching and replacement in this file
+automatic-linker-disable-url-title: true
+
 # Define aliases for this file (standard Obsidian feature)
 aliases: [shortname, alternative-name]
 ---
@@ -298,16 +321,6 @@ src/
 └── update-editor.ts           # Editor update utilities
 ```
 
-## Performance
-
-The plugin uses a Trie data structure for efficient file name matching, making it performant even with thousands of files. Link conversion is optimized to handle large vaults without noticeable lag.
-
-## Known Limitations
-
-- URL title fetching requires network access and may be slow for many URLs
-- Proximity-based Linking requires files to be indexed (restart may be needed after adding many files)
-- Alias consideration requires plugin restart when toggled in settings
-
 ## Troubleshooting
 
 **Links aren't being created:**
@@ -316,8 +329,7 @@ The plugin uses a Trie data structure for efficient file name matching, making i
 
 **Proximity-based Linking not working:**
 - Ensure "Proximity-based Linking" is enabled in settings
-- Restart Obsidian after changing base directory settings
-- Check that files are within the configured base directory
+- Check that files are within Obsidian's configured "Folder to create new notes in" directory if the "Respect 'Folder to create new notes in' setting" option is enabled
 
 **Conflicts with Obsidian Linter:**
 - Follow the integration guide above to run plugins in sequence

docs/superpowers/plans/2026-07-17-settings-grouping.md

@@ -0,0 +1,713 @@
+# Settings Grouping Implementation Plan
+
+> **For agentic workers:** REQUIRED SUB-SKILL: Use superpowers:subagent-driven-development (recommended) or superpowers:executing-plans to implement this plan task-by-task. Steps use checkbox (`- [ ]`) syntax for tracking.
+
+**Goal:** 設定画面と README の28設定を、利用目的に基づく同一の6グループへ再編する。
+
+**Architecture:** SETTINGS_CATALOG を設定画面のグループ名と表示順の単一の情報源として維持し、既存の PluginSettingTab はそのカタログを機械的に描画する。保存キー、既定値、制御種別、更新処理は変えず、README の Configuration だけを同じ分類へ同期する。
+
+**Tech Stack:** TypeScript、Obsidian Plugin API、Vitest、ESLint、npm、GitButler CLI。
+
+## Global Constraints
+
+- 各設定項目のキー、表示名、説明文、既定値を変更しない。
+- 設定値の保存形式、読み込み処理、実行時動作を変更しない。
+- 折りたたみ、タブ、入れ子の見出し、独自 CSS、依存関係による表示切り替えを追加しない。
+- 設定画面と README は、同じ6グループ、同じ所属、同じ順序を持つ。
+- README の Configuration は28個の永続設定だけを列挙する。
+- automatic-linker-disable-url-title は Configuration から重複を除き、既存の Frontmatter Options で引き続き説明する。
+- AGENTS.md の既存変更は今回のコミットへ含めない。
+- バージョン管理の書き込みには but を使う。
+- コミットは英語の Conventional Commits とし、Why と What を本文に記載する。
+- GitHub URL へ直接アクセスしない。
+
+---
+
+## File Structure
+
+- Modify: src/settings/__tests__/settings-catalog.test.ts
+  - グループ名、所属、表示順、グループの連続性を一つの期待値で固定する。
+  - テキストエリアのサイズ指定テストを、表示順から独立した検証へ直す。
+- Modify: src/settings/settings-catalog.ts
+  - 既存の28エントリを6つの連続したグループへ並べ替える。
+  - group 以外のメタデータは変更しない。
+- Modify: README.md
+  - Configuration を設定画面と同じ6見出し、同じ設定順へ置き換える。
+  - 未掲載の Match sentence case、Ignore headings、Ignore Markdown tables を追加する。
+
+---
+
+### Task 1: 設定カタログのグループ契約
+
+**Files:**
+- Modify: src/settings/__tests__/settings-catalog.test.ts:10-44
+- Modify: src/settings/settings-catalog.ts:81-352
+- Test: src/settings/__tests__/settings-catalog.test.ts
+
+**Interfaces:**
+- Consumes: 既存の SETTINGS_CATALOG と DEFAULT_SETTINGS。
+- Produces: 既存の readonly SettingCatalogEntry[] インターフェースを保った、6グループの連続した設定カタログ。
+- Produces: 設定タブが先頭から描画できる確定済みの表示順。
+
+- [ ] **Step 1: グループ構成を固定する失敗テストを書く**
+
+src/settings/__tests__/settings-catalog.test.ts のカタログ網羅テスト直後へ、次のテストを追加する。
+
+~~~ts
+it("groups settings by user workflow in display order", () => {
+    const expectedGroups = [
+        {
+            group: "Formatting Workflow",
+            keys: [
+                "formatOnSave",
+                "formatDelayMs",
+                "runPrettierAfterFormatting",
+                "runLinterAfterFormatting",
+            ],
+        },
+        {
+            group: "Link Behavior",
+            keys: [
+                "respectNewFileFolderPath",
+                "proximityBasedLinking",
+                "includeAliases",
+                "removeAliasInDirs",
+                "ignoreCase",
+                "matchSentenceCase",
+            ],
+        },
+        {
+            group: "Exclusions",
+            keys: [
+                "preventSelfLinking",
+                "ignoreDateFormats",
+                "ignoreHeadings",
+                "ignoreMarkdownTables",
+                "excludeDirsFromAutoLinking",
+            ],
+        },
+        {
+            group: "URL Formatting",
+            keys: [
+                "formatGitHubURLs",
+                "githubEnterpriseURLs",
+                "formatJiraURLs",
+                "jiraURLs",
+                "formatLinearURLs",
+                "replaceUrlWithTitle",
+                "replaceUrlWithTitleIgnoreDomains",
+            ],
+        },
+        {
+            group: "AI Link Enhancement (Beta)",
+            keys: [
+                "aiEnabled",
+                "aiEndpoint",
+                "aiModel",
+                "aiMaxContext",
+            ],
+        },
+        {
+            group: "Diagnostics",
+            keys: ["showNotice", "debug"],
+        },
+    ]
+
+    const actualGroups = SETTINGS_CATALOG.reduce<Array<{
+        group: string
+        keys: Array<keyof typeof DEFAULT_SETTINGS>
+    }>>((groups, entry) => {
+        const currentGroup = groups[groups.length - 1]
+        if (currentGroup?.group === entry.group) {
+            currentGroup.keys.push(entry.key)
+            return groups
+        }
+
+        groups.push({
+            group: entry.group,
+            keys: [entry.key],
+        })
+        return groups
+    }, [])
+
+    expect(actualGroups).toEqual(expectedGroups)
+})
+~~~
+
+同じファイルのテキストエリアサイズ検証は、表示順ではなく対象キーだけを検証する形へ置き換える。
+
+~~~ts
+it("marks only the URL textarea settings for explicit sizing", () => {
+    const sizedTextareaKeys = SETTINGS_CATALOG
+        .filter(entry => entry.control === "textarea")
+        .filter(entry => (entry as { rows?: number }).rows === 4)
+        .filter(entry => (entry as { cols?: number }).cols === 50)
+        .map(entry => entry.key)
+        .sort()
+
+    expect(sizedTextareaKeys).toEqual([
+        "githubEnterpriseURLs",
+        "jiraURLs",
+        "replaceUrlWithTitleIgnoreDomains",
+    ])
+})
+~~~
+
+- [ ] **Step 2: 集中的なテストを実行して RED を確認する**
+
+Run:
+
+~~~bash
+npm run test -- src/settings/__tests__/settings-catalog.test.ts
+~~~
+
+Expected: FAIL。
+
+groups settings by user workflow in display order が、現在の Formatting、Integrations、サービス別 URL グループとの差分を報告する。
+
+- [ ] **Step 3: SETTINGS_CATALOG を承認済みの順序へ置き換える**
+
+src/settings/settings-catalog.ts の SETTINGS_CATALOG 定義全体を、次の内容へ置き換える。
+
+~~~ts
+export const SETTINGS_CATALOG = [
+    {
+        key: "formatOnSave",
+        group: "Formatting Workflow",
+        name: "Format on save",
+        description:
+            "When enabled, the file will be automatically formatted (links replaced) when saving.",
+        control: "toggle",
+        refreshesIndex: false,
+    },
+    {
+        key: "formatDelayMs",
+        group: "Formatting Workflow",
+        name: "Format delay (ms)",
+        description:
+            "Delay in milliseconds before formatting. Increase this value if the linter/prettier runs before the file is fully saved.",
+        control: "text",
+        placeholder: "e.g. 100",
+        refreshesIndex: false,
+    },
+    {
+        key: "runPrettierAfterFormatting",
+        group: "Formatting Workflow",
+        name: "Run Prettier after formatting",
+        description:
+            "When enabled, Prettier will be executed after Automatic Linker formatting. This requires prettier-format plugin to be installed. https://github.com/dylanarmstrong/obsidian-prettier-plugin",
+        control: "toggle",
+        refreshesIndex: false,
+    },
+    {
+        key: "runLinterAfterFormatting",
+        group: "Formatting Workflow",
+        name: "Run Obsidian Linter after formatting",
+        description:
+            "When enabled, Obsidian Linter will be executed after Automatic Linker formatting. This requires the Obsidian Linter plugin to be installed.",
+        control: "toggle",
+        refreshesIndex: false,
+    },
+    {
+        key: "respectNewFileFolderPath",
+        group: "Link Behavior",
+        name: "Respect 'Folder to create new notes in' setting",
+        description:
+            "When enabled, the plugin will use Obsidian's 'Folder to create new notes in' setting as the base directory for omitting folder prefixes in links.",
+        control: "toggle",
+        refreshesIndex: true,
+    },
+    {
+        key: "proximityBasedLinking",
+        group: "Link Behavior",
+        name: "Proximity-based linking",
+        description:
+            "When enabled, the plugin will automatically resolve namespaces for shorthand links. If multiple candidates share the same shorthand, the candidate with the most common path segments relative to the current file will be selected.",
+        control: "toggle",
+        refreshesIndex: true,
+    },
+    {
+        key: "includeAliases",
+        group: "Link Behavior",
+        name: "Include aliases",
+        description:
+            "When enabled, aliases will be included when processing links. Note: A restart is required for changes to take effect.",
+        control: "toggle",
+        refreshesIndex: true,
+    },
+    {
+        key: "removeAliasInDirs",
+        group: "Link Behavior",
+        name: "Remove aliases in directories",
+        description:
+            "Directories where link aliases should be removed, one per line (e.g. 'dir' will convert [[dir/xxx|yyy]] to [[dir/xxx]]). This affects both auto-generated aliases and frontmatter aliases.",
+        control: "textarea",
+        placeholder: "dir1\ndir2/subdir",
+        multiline: true,
+        refreshesIndex: true,
+    },
+    {
+        key: "ignoreCase",
+        group: "Link Behavior",
+        name: "Ignore case",
+        description:
+            "When enabled, link matching will be case-insensitive. The original case of the text will be preserved in the link.",
+        control: "toggle",
+        refreshesIndex: true,
+    },
+    {
+        key: "matchSentenceCase",
+        group: "Link Behavior",
+        name: "Match sentence case",
+        description:
+            "When 'Ignore case' is OFF, match text that is capitalized at the start of a sentence. For example, 'My name' at a sentence start will match the file 'my name'. This setting is ignored when 'Ignore case' is ON.",
+        control: "toggle",
+        refreshesIndex: false,
+    },
+    {
+        key: "preventSelfLinking",
+        group: "Exclusions",
+        name: "Prevent self-linking",
+        description:
+            "When enabled, text will not be linked to its own file. For example, the word 'VPN' inside VPN.md will not be converted to a link.",
+        control: "toggle",
+        refreshesIndex: true,
+    },
+    {
+        key: "ignoreDateFormats",
+        group: "Exclusions",
+        name: "Ignore date formats",
+        description:
+            "When enabled, links that match date formats (e.g. 2025-02-10) will be ignored. This helps maintain compatibility with Obsidian Tasks.",
+        control: "toggle",
+        refreshesIndex: true,
+    },
+    {
+        key: "ignoreHeadings",
+        group: "Exclusions",
+        name: "Ignore headings",
+        description:
+            "When enabled, headings (lines starting with #) will not have links added to them.",
+        control: "toggle",
+        refreshesIndex: false,
+    },
+    {
+        key: "ignoreMarkdownTables",
+        group: "Exclusions",
+        name: "Ignore Markdown tables",
+        description:
+            "When enabled, Markdown table rows will not have links added to them.",
+        control: "toggle",
+        refreshesIndex: false,
+    },
+    {
+        key: "excludeDirsFromAutoLinking",
+        group: "Exclusions",
+        name: "Exclude directories from automatic linking",
+        description:
+            "Directories to be excluded from automatic linking, one per line (e.g. 'Templates')",
+        control: "textarea",
+        placeholder: "Templates\nArchive",
+        multiline: true,
+        refreshesIndex: true,
+    },
+    {
+        key: "formatGitHubURLs",
+        group: "URL Formatting",
+        name: "Format GitHub URLs on save",
+        description:
+            "When enabled, GitHub URLs will be formatted when saving the file.",
+        control: "toggle",
+        refreshesIndex: false,
+    },
+    {
+        key: "githubEnterpriseURLs",
+        group: "URL Formatting",
+        name: "GitHub Enterprise URLs",
+        description:
+            "Add your GitHub Enterprise URLs, one per line (e.g. github.enterprise.com)",
+        control: "textarea",
+        placeholder: "github.enterprise.com\ngithub.company.com",
+        multiline: true,
+        rows: 4,
+        cols: 50,
+        refreshesIndex: false,
+    },
+    {
+        key: "formatJiraURLs",
+        group: "URL Formatting",
+        name: "Format JIRA URLs on save",
+        description:
+            "When enabled, JIRA URLs will be formatted when saving the file.",
+        control: "toggle",
+        refreshesIndex: false,
+    },
+    {
+        key: "jiraURLs",
+        group: "URL Formatting",
+        name: "JIRA URLs",
+        description:
+            "Add your JIRA URLs, one per line (e.g. jira.enterprise.com)",
+        control: "textarea",
+        placeholder: "jira.enterprise.com\njira.company.com",
+        multiline: true,
+        rows: 4,
+        cols: 50,
+        refreshesIndex: false,
+    },
+    {
+        key: "formatLinearURLs",
+        group: "URL Formatting",
+        name: "Format Linear URLs on save",
+        description:
+            "When enabled, Linear URLs will be formatted when saving the file.",
+        control: "toggle",
+        refreshesIndex: false,
+    },
+    {
+        key: "replaceUrlWithTitle",
+        group: "URL Formatting",
+        name: "Replace URL with title",
+        description:
+            "When enabled, raw URLs will be replaced with [Page Title](URL). Requires fetching the URL content.",
+        control: "toggle",
+        refreshesIndex: false,
+    },
+    {
+        key: "replaceUrlWithTitleIgnoreDomains",
+        group: "URL Formatting",
+        name: "Ignore domains",
+        description:
+            "Ignore domains for replacing URLs with titles, one per line (e.g. x.com)",
+        control: "textarea",
+        placeholder: "",
+        multiline: true,
+        rows: 4,
+        cols: 50,
+        refreshesIndex: false,
+    },
+    {
+        key: "aiEnabled",
+        group: "AI Link Enhancement (Beta)",
+        name: "Enable AI Link Enhancement",
+        description:
+            "When enabled, an AI-powered link enhancer command will be available. It uses a local LLM to resolve ambiguous links and correct existing ones.",
+        control: "toggle",
+        refreshesIndex: false,
+    },
+    {
+        key: "aiEndpoint",
+        group: "AI Link Enhancement (Beta)",
+        name: "AI API Endpoint",
+        description:
+            "The URL of your OpenAI-compatible AI server (e.g. LM Studio, Ollama).",
+        control: "text",
+        placeholder: "http://localhost:1234/v1",
+        refreshesIndex: false,
+    },
+    {
+        key: "aiModel",
+        group: "AI Link Enhancement (Beta)",
+        name: "AI Model",
+        description: "The name of the model to use (e.g. gemma-4-7b).",
+        control: "text",
+        placeholder: "gemma-4-7b",
+        refreshesIndex: false,
+    },
+    {
+        key: "aiMaxContext",
+        group: "AI Link Enhancement (Beta)",
+        name: "Max Context Length",
+        description:
+            "Number of characters around the link to provide as context to the AI.",
+        control: "text",
+        placeholder: "500",
+        refreshesIndex: false,
+    },
+    {
+        key: "showNotice",
+        group: "Diagnostics",
+        name: "Show load notice",
+        description: "Display a notice when markdown files are loaded.",
+        control: "toggle",
+        refreshesIndex: false,
+    },
+    {
+        key: "debug",
+        group: "Diagnostics",
+        name: "Debug mode",
+        description:
+            "When enabled, debug information will be logged to the console.",
+        control: "toggle",
+        refreshesIndex: false,
+    },
+] as const satisfies readonly SettingCatalogEntry[]
+~~~
+
+- [ ] **Step 4: 集中的なテストを実行して GREEN を確認する**
+
+Run:
+
+~~~bash
+npm run test -- src/settings/__tests__/settings-catalog.test.ts
+~~~
+
+Expected: PASS。
+
+Vitest が1ファイル、6テストの成功を報告する。
+
+- [ ] **Step 5: 型検査を実行する**
+
+Run:
+
+~~~bash
+npm run tsc
+~~~
+
+Expected: exit code 0。
+
+- [ ] **Step 6: カタログとテストだけをコミットする**
+
+Run:
+
+~~~bash
+but diff
+~~~
+
+出力から src/settings/settings-catalog.ts と src/settings/__tests__/settings-catalog.test.ts のファイル ID を取得する。
+その2 ID だけを --changes へ渡し、次のメッセージで settings-grouping ブランチへコミットする。
+
+~~~text
+refactor(settings): group options by user workflow
+
+Why:
+- The settings tab mixes unrelated options under broad or service-specific headings.
+
+What:
+- Reorder the catalog into six contiguous user-facing groups.
+- Lock group membership and display order with a focused test.
+~~~
+
+Expected: コミット結果に上記2ファイルだけが含まれ、AGENTS.md は uncommitted に残る。
+
+---
+
+### Task 2: README の設定分類
+
+**Files:**
+- Modify: README.md:98-142
+
+**Interfaces:**
+- Consumes: Task 1 が確定した6グループと28設定の順序。
+- Produces: 設定画面と同じ見出し、所属、順序を持つ Configuration。
+- Produces: automatic-linker-disable-url-title の説明を既存の Frontmatter Options に一箇所だけ残した README。
+
+- [ ] **Step 1: Configuration を6グループへ置き換える**
+
+README.md の Configuration 見出しから Usage Examples の直前までを、次の内容へ置き換える。
+
+~~~markdown
+## Configuration
+
+### Formatting Workflow
+
+- **Format on save**: Automatically format links when saving files.
+- **Format delay (ms)**: Delay formatting and post-format integrations by the configured number of milliseconds.
+- **Run Prettier after formatting**: Run the Prettier plugin after Automatic Linker formatting.
+- **Run Obsidian Linter after formatting**: Run Obsidian Linter after Automatic Linker formatting.
+
+### Link Behavior
+
+- **Respect 'Folder to create new notes in' setting**: Use Obsidian's new-note folder as the base directory when omitting folder prefixes from links.
+- **Proximity-based linking**: Resolve shorthand links to the candidate with the most path segments in common with the current file.
+- **Include aliases**: Include frontmatter aliases when matching text.
+- **Remove aliases in directories**: Remove displayed link aliases for links targeting the configured directories.
+- **Ignore case**: Match links without requiring the same letter case.
+- **Match sentence case**: When Ignore case is disabled, match text capitalized only because it starts a sentence.
+
+### Exclusions
+
+- **Prevent self-linking**: Do not link text to the current file.
+- **Ignore date formats**: Skip date-formatted text such as `2025-02-10`.
+- **Ignore headings**: Do not add links inside Markdown headings.
+- **Ignore Markdown tables**: Do not add links inside Markdown table rows.
+- **Exclude directories from automatic linking**: Skip files in the configured directories when building automatic links.
+
+### URL Formatting
+
+- **Format GitHub URLs on save**: Convert GitHub URLs to readable issue and pull-request links.
+- **GitHub Enterprise URLs**: Add custom GitHub Enterprise domains.
+- **Format JIRA URLs on save**: Convert JIRA issue URLs to readable links.
+- **JIRA URLs**: Add custom JIRA domains.
+- **Format Linear URLs on save**: Convert Linear issue URLs to readable links.
+- **Replace URL with title**: Replace bare URLs with Markdown links using fetched page titles.
+- **Ignore domains**: Exclude configured domains from URL title replacement.
+
+### AI Link Enhancement (Beta)
+
+- **Enable AI Link Enhancement**: Add a command that uses a local LLM to resolve and correct ambiguous links.
+- **AI API Endpoint**: Set the URL of the OpenAI-compatible local AI server.
+- **AI Model**: Set the model name sent to the local AI server.
+- **Max Context Length**: Set the number of surrounding characters sent for each ambiguous link.
+
+### Diagnostics
+
+- **Show load notice**: Display a notice after the plugin loads Markdown files into its index.
+- **Debug mode**: Log debug information to the developer console.
+~~~
+
+Frontmatter Options 以下の automatic-linker-disable-url-title の説明は変更しない。
+
+- [ ] **Step 2: 見出しの順序を確認する**
+
+Run:
+
+~~~bash
+sed -n '/^## Configuration$/,/^## Usage Examples$/p' README.md | rg '^### '
+~~~
+
+Expected:
+
+~~~text
+### Formatting Workflow
+### Link Behavior
+### Exclusions
+### URL Formatting
+### AI Link Enhancement (Beta)
+### Diagnostics
+~~~
+
+- [ ] **Step 3: Configuration が28設定を一度ずつ列挙することを確認する**
+
+Run:
+
+~~~bash
+sed -n '/^## Configuration$/,/^## Usage Examples$/p' README.md | rg -c '^- \*\*'
+~~~
+
+Expected:
+
+~~~text
+28
+~~~
+
+- [ ] **Step 4: 未掲載だった3設定を確認する**
+
+Run:
+
+~~~bash
+sed -n '/^## Configuration$/,/^## Usage Examples$/p' README.md | rg 'Match sentence case|Ignore headings|Ignore Markdown tables'
+~~~
+
+Expected:
+
+~~~text
+- **Match sentence case**: When Ignore case is disabled, match text capitalized only because it starts a sentence.
+- **Ignore headings**: Do not add links inside Markdown headings.
+- **Ignore Markdown tables**: Do not add links inside Markdown table rows.
+~~~
+
+- [ ] **Step 5: frontmatter の URL タイトル無効化手段が一箇所に残ることを確認する**
+
+Run:
+
+~~~bash
+rg -c 'automatic-linker-disable-url-title' README.md
+~~~
+
+Expected:
+
+~~~text
+1
+~~~
+
+- [ ] **Step 6: README だけをコミットする**
+
+Run:
+
+~~~bash
+but diff
+~~~
+
+出力から README.md のファイル ID を取得する。
+その ID だけを --changes へ渡し、次のメッセージで settings-grouping ブランチへコミットする。
+
+~~~text
+docs(settings): align configuration with grouped options
+
+Why:
+- Readers currently see categories and option coverage that differ from the settings tab.
+
+What:
+- Mirror the six settings groups and their display order in the README.
+- Document the three previously omitted settings.
+~~~
+
+Expected: コミット結果に README.md だけが含まれ、AGENTS.md は uncommitted に残る。
+
+---
+
+### Task 3: 回帰検証
+
+**Files:**
+- Verify: src/settings/settings-catalog.ts
+- Verify: src/settings/__tests__/settings-catalog.test.ts
+- Verify: README.md
+
+**Interfaces:**
+- Consumes: Task 1 の設定カタログと Task 2 の README。
+- Produces: 既存の保存形式と実行時動作を維持した、検証済みの設定グルーピング変更。
+
+- [ ] **Step 1: 設定カタログのテストを再実行する**
+
+Run:
+
+~~~bash
+npm run test -- src/settings/__tests__/settings-catalog.test.ts
+~~~
+
+Expected: PASS。
+
+Vitest が1ファイル、6テストの成功を報告する。
+
+- [ ] **Step 2: 全テストを実行する**
+
+Run:
+
+~~~bash
+npm run test -- --reporter=dot
+~~~
+
+Expected: exit code 0 で全テストが成功する。
+
+- [ ] **Step 3: 型検査を実行する**
+
+Run:
+
+~~~bash
+npm run tsc
+~~~
+
+Expected: exit code 0。
+
+- [ ] **Step 4: lint を実行する**
+
+Run:
+
+~~~bash
+npm run lint
+~~~
+
+Expected: exit code 0。
+
+- [ ] **Step 5: 意図しない未コミット変更がないことを確認する**
+
+Run:
+
+~~~bash
+but diff
+~~~
+
+Expected: src/settings/settings-catalog.ts、src/settings/__tests__/settings-catalog.test.ts、README.md は表示されない。
+
+今回の作業前から存在する AGENTS.md の変更だけが uncommitted に残る。

docs/superpowers/specs/2026-06-22-architecture-deepening-design.md

@@ -0,0 +1,277 @@
+# Architecture Deepening Design
+
+## Goal
+
+Deepen the architecture of Obsidian Automatic Linker without changing user-visible behavior.
+
+The work should reduce duplicated transformation logic, move Obsidian-specific code toward thin adapters, and concentrate link-formatting behavior in modules with higher locality and leverage.
+
+## Scope
+
+Implement all five architecture-review candidates in a staged sequence:
+
+1. Deepen candidate scanning.
+2. Deepen the formatting run.
+3. Deepen the settings catalog.
+4. Deepen Markdown protected segments.
+5. Deepen URL formatting adapters.
+
+Each stage must preserve the existing behavior covered by the current test suite. New tests should be added before production changes when a stage exposes behavior that is currently duplicated, underspecified, or hard to test through the existing interface.
+
+## Non-Goals
+
+- Do not add new user-facing features.
+- Do not change existing settings names, defaults, command ids, or manifest metadata.
+- Do not change Obsidian link output formats except where an existing test already expects that behavior.
+- Do not replace the current test framework or build tooling.
+- Do not introduce a Markdown parser dependency unless a later implementation step proves regex segmentation cannot preserve current behavior.
+
+## Architecture
+
+The current codebase has two large centers of gravity:
+
+- `src/main.ts` owns Obsidian lifecycle, command registration, settings access, indexing, URL title fetching, URL formatting, link replacement, and AI command orchestration.
+- `src/replace-links/replace-links.ts` owns a deep but broad implementation for link candidate matching and content transformation.
+
+The target architecture keeps the transformation core pure and moves app integration to adapters:
+
+- Obsidian commands, editor reads/writes, notices, network requests, and plugin lifecycle remain in adapter code.
+- Link candidate scanning, Markdown segment protection, URL formatting, settings projection, and formatting-run sequencing become testable modules.
+- Existing modules are split only where the split concentrates complexity behind a smaller interface.
+
+## Candidate 1: Deepen Candidate Scanning
+
+### Problem
+
+`replaceLinks` and `resolveAmbiguities` both scan note text for possible link candidates.
+
+`replaceLinks` contains the full implementation: protected spans, trie traversal, CJK handling, sentence-case matching, namespace scope, table awareness, and existing-link correction. `resolveAmbiguities` contains a simplified scanner for AI requests. This weakens locality because changing candidate matching requires checking two implementations.
+
+### Design
+
+Create a candidate scanning module used by both link replacement and AI ambiguity resolution.
+
+The module should expose occurrences of linkable text and existing links in terms of the existing data model:
+
+- source text range
+- matched text
+- candidate key
+- candidate data
+- whether the occurrence is protected, replaceable, or an existing wikilink
+- enough context for AI request construction
+
+`replaceLinks` remains responsible for rendering replacements. `resolveAmbiguities` becomes an adapter that asks the scanner for ambiguous occurrences and sends them to the AI client.
+
+### Testing
+
+Tests should prove that AI ambiguity detection respects the same candidate matching rules as replacement for:
+
+- protected inline code
+- existing Markdown links
+- case-insensitive candidates
+- namespace-scoped candidates
+- CJK or sentence-case behavior where currently covered by `replaceLinks`
+
+## Candidate 2: Deepen The Formatting Run
+
+### Problem
+
+`main.ts` currently sequences multiple pure transformations directly:
+
+- GitHub URL formatting
+- Jira URL formatting
+- Linear URL formatting
+- URL title replacement
+- frontmatter/body splitting
+- link replacement
+- settings projection for `replaceLinks`
+
+The file and selection commands duplicate the settings projection. The AI command passes a broader settings object into `replaceLinks`, which makes the transformation interface inconsistent.
+
+### Design
+
+Create a formatting-run module that owns content transformation sequencing.
+
+The Obsidian plugin adapter should supply:
+
+- current file path
+- raw content or selected text
+- frontmatter when available
+- candidate index
+- URL title map
+- link generator
+- projected runtime settings
+
+The formatting-run module should return transformed text and avoid direct Obsidian dependencies.
+
+`main.ts` keeps editor reads/writes, command registration, notices, vault traversal, URL title fetching, and plugin integration.
+
+### Testing
+
+Tests should exercise the formatting run without constructing `AutomaticLinkerPlugin` or mocking Obsidian. Move the existing `main.ts` tests that only verify pure transformation behavior to formatting-run tests; keep `main.ts` tests only for Obsidian adapter behavior such as link generator integration.
+
+## Candidate 3: Deepen The Settings Catalog
+
+### Problem
+
+Adding a setting currently crosses several places:
+
+- `src/settings/settings-info.ts`
+- `src/settings/settings.ts`
+- `src/main.ts`
+- `src/replace-links/replace-links.ts`
+
+The repo's development guide already warns about this. That warning is evidence that the settings module is shallow: the interface nearly matches the implementation, and adding a field lacks locality.
+
+### Design
+
+Create a settings catalog module that owns settings metadata and projections.
+
+The catalog should centralize:
+
+- default values
+- setting groups and display metadata used by the settings tab
+- whether changing a setting requires index refresh
+- projection from `AutomaticLinkerSettings` to link replacement settings
+- projection from `AutomaticLinkerSettings` to URL formatting adapter settings, including format flags and configured domains
+
+The settings tab remains an Obsidian UI adapter that renders catalog entries into `Setting` controls.
+
+### Testing
+
+Tests should cover:
+
+- every default setting has catalog metadata or an explicit reason it is runtime-only
+- link replacement projection includes all fields expected by `ReplaceLinksSettings`
+- refresh-required settings match current behavior
+
+## Candidate 4: Deepen Markdown Protected Segments
+
+### Problem
+
+Markdown protection rules appear in multiple modules:
+
+- `replaceLinks` protects code blocks, inline code, existing wikilinks, Markdown links, headings, tables, and callouts.
+- URL title replacement and URL discovery perform their own context checks.
+
+The URL title module also documents an incomplete fenced-code check. This is locality friction and an opportunity to put Markdown segmentation behind one module.
+
+### Design
+
+Create a Markdown segment module that divides text into transformable prose and protected segments.
+
+The module should preserve exact text and ordering. Adapters can then transform only prose segments:
+
+- link replacement adapter
+- URL discovery adapter
+- URL title replacement adapter
+
+This stage should be conservative. First extract fenced code, inline code, Markdown links, and wikilinks. Then add headings, tables, and callouts to the same module after exact round-trip segment tests are passing.
+
+### Testing
+
+Tests should cover exact round-trip reconstruction and per-segment transformation for:
+
+- inline code
+- fenced code blocks, including unclosed fences
+- existing wikilinks
+- Markdown links
+- headings when ignored
+- Markdown tables when ignored
+- Obsidian callouts
+
+## Candidate 5: Deepen URL Formatting Adapters
+
+### Problem
+
+URL formatting has separate adapter modules for GitHub, Jira, and Linear, but orchestration is split:
+
+- `main.ts` chooses individual passes.
+- `replaceURLs` runs a formatter over URL matches.
+- `github.ts` imports sibling formatters through `formatURL`, creating adapter coupling.
+
+This is a shallow seam: there are already multiple adapters, but the module that should own ordering and one pass over URLs does not yet own them fully.
+
+### Design
+
+Create a URL formatting module that owns:
+
+- URL discovery in transformable prose
+- adapter ordering
+- selecting the first adapter that changes a URL
+- preserving current output formats
+
+GitHub, Jira, and Linear modules become independent adapters. They should not import each other.
+
+### Testing
+
+Tests should prove:
+
+- all existing GitHub, Jira, and Linear outputs remain unchanged
+- a text body can be processed in one URL formatting call
+- adapter ordering is deterministic
+- disabled settings prevent matching adapters from changing text
+
+## Data Flow
+
+The target formatting flow is:
+
+1. Obsidian adapter reads active file, selection, or vault file.
+2. Obsidian adapter gathers frontmatter, candidate index, settings, URL title map, and link generator.
+3. Formatting-run module splits frontmatter from body when needed.
+4. Formatting-run module runs URL formatting, URL title replacement, and link replacement using pure modules.
+5. Obsidian adapter writes the result back to the editor or vault.
+6. Optional plugin integrations such as Prettier and Obsidian Linter remain in `main.ts`.
+
+## Error Handling
+
+Preserve current error behavior:
+
+- Obsidian command callbacks catch and log unexpected errors.
+- URL title fetching failures are logged only when debug mode is enabled.
+- AI API errors continue to surface through the AI command catch block and notice.
+- Pure transformation modules should not create `Notice` instances or call Obsidian APIs.
+
+## Test Strategy
+
+Use TDD for each implementation stage.
+
+The expected test layers are:
+
+- pure module tests for candidate scanning, Markdown segmentation, formatting run, settings projection, and URL formatting orchestration
+- existing integration-style tests around `AutomaticLinkerPlugin` only where Obsidian adapter behavior is the subject
+- full regression suite after each stage
+
+The baseline regression command is:
+
+```bash
+npm run test -- --reporter=dot
+```
+
+## Migration Strategy
+
+Each stage should be reversible and independently reviewable.
+
+1. Add tests for the behavior being centralized.
+2. Add the new module with minimal implementation.
+3. Route one existing caller through the new module.
+4. Run focused tests.
+5. Route the second caller through the same module.
+6. Run the full test suite.
+7. Commit the stage.
+
+## Risks
+
+- Candidate scanning is the highest-risk stage because it touches the most behavior in `replaceLinks`.
+- Markdown segmentation can accidentally change exact output if placeholder restoration differs from current code.
+- Settings catalog work can create broad churn in `settings.ts`; keep the UI adapter mechanical and avoid visual changes.
+- URL formatting must preserve current output strings, including the existing link icon and Enterprise URL handling.
+
+## Success Criteria
+
+- All current tests pass after each stage.
+- `main.ts` no longer owns pure transformation sequencing.
+- `resolveAmbiguities` no longer has a separate simplified candidate scanner.
+- Link replacement settings projection exists in one place.
+- URL formatting can process all configured adapters through one module call.
+- Git status shows only intentional source, test, and documentation changes for each stage.

docs/superpowers/specs/2026-07-17-settings-grouping-design.md

@@ -0,0 +1,112 @@
+# 設定項目グルーピング設計
+
+## 背景
+
+設定画面には見出しがあるものの、`Formatting` に12項目が集中し、URL関連の設定はサービスごとの小さな見出しに分かれている。
+
+README の Configuration には別の分類があり、`Ignore headings`、`Ignore Markdown tables`、`Match sentence case` の3項目が掲載されていない。
+この状態では、利用者が同じ設定を画面と README で異なる場所から探すことになる。
+
+## 目的
+
+設定を利用目的に基づく6グループへ再編し、設定画面と README で見出し、所属項目、表示順を一致させる。
+
+## 対象範囲
+
+- `SETTINGS_CATALOG` のグループ名と項目順を変更する。
+- README の Configuration を同じグループ構成へ変更する。
+- README に未掲載の3項目を追加する。
+- グループ構成と連続性をテストで固定する。
+
+## 対象外
+
+- 各設定項目のキー、表示名、説明文、既定値は変更しない。
+- 設定値の保存形式や読み込み処理は変更しない。
+- 設定の実行時動作は変更しない。
+- 折りたたみ、タブ、入れ子の見出し、独自 CSS は追加しない。
+- 設定間の依存関係に応じた表示切り替えは追加しない。
+
+## グループ構成
+
+設定画面と README は、次の順序と所属を共有する。
+
+| グループ | 設定項目 |
+|---|---|
+| **Formatting Workflow** | Format on save、Format delay (ms)、Run Prettier after formatting、Run Obsidian Linter after formatting |
+| **Link Behavior** | Respect 'Folder to create new notes in' setting、Proximity-based linking、Include aliases、Remove aliases in directories、Ignore case、Match sentence case |
+| **Exclusions** | Prevent self-linking、Ignore date formats、Ignore headings、Ignore Markdown tables、Exclude directories from automatic linking |
+| **URL Formatting** | Format GitHub URLs on save、GitHub Enterprise URLs、Format JIRA URLs on save、JIRA URLs、Format Linear URLs on save、Replace URL with title、Ignore domains |
+| **AI Link Enhancement (Beta)** | Enable AI Link Enhancement、AI API Endpoint、AI Model、Max Context Length |
+| **Diagnostics** | Show load notice、Debug mode |
+
+`Formatting Workflow` は、整形の起動から後続プラグインの実行までを一つの流れとして扱う。
+`Format delay (ms)` は保存時の整形開始と Prettier、Obsidian Linter の実行前に使われるため、このグループに置く。
+
+`Link Behavior` は、候補の照合、名前空間の解決、生成する Wiki リンクの表現を扱う。
+`Remove aliases in directories` はリンク対象を除外せず、生成結果の表現を変えるため、このグループに置く。
+
+`Exclusions` は、リンクを生成しない対象を集める。
+`Prevent self-linking` も現在のファイルを候補から除く規則なので、このグループに置く。
+
+`URL Formatting` は、サービス固有の URL 整形と汎用的なタイトル置換をまとめる。
+サービス固有の設定を先に置き、汎用的な `Replace URL with title` と `Ignore domains` をその後に置く。
+
+## 設定画面
+
+設定画面は既存の `Setting.setHeading()` による見出し描画を維持する。
+`SETTINGS_CATALOG` では同じグループの項目を一つの連続したブロックに並べ、グループが再登場する構造を許さない。
+
+グループを変えても各項目が参照する設定キーは変わらない。
+入力値は従来どおり保存され、インデックス更新や URL タイトルマップ更新の条件も維持される。
+
+## README
+
+README の Configuration は設定画面と同じ6見出し、同じ順序へ変更する。
+各見出しでは設定画面と同じ順序で項目を説明し、現在未掲載の次の3項目を `Link Behavior` または `Exclusions` に追加する。
+
+- `Match sentence case` は `Link Behavior` に追加する。
+- `Ignore headings` は `Exclusions` に追加する。
+- `Ignore Markdown tables` は `Exclusions` に追加する。
+
+`Frontmatter URL Title Opt-out` は保存設定ではなく、README 後半の Frontmatter Options にも記載されている。
+Configuration から重複する説明を除き、Frontmatter Options の説明は維持する。
+
+## データの流れ
+
+1. `SETTINGS_CATALOG` が各設定のグループと表示順を定義する。
+2. 設定タブがカタログを先頭から読み、グループの境界で見出しを描画する。
+3. 各設定コントロールは従来と同じキーを通じて値を保存する。
+4. README が同じ分類を利用者向けの説明として記録する。
+
+## エラー処理
+
+設定カタログの静的な表示メタデータと README だけを変更するため、新しい実行時エラーは発生しない。
+既存の入力値検証、保存失敗時の挙動、インデックス更新処理は変更しない。
+
+## テスト方針
+
+既存の「すべての既定設定がカタログに一度ずつ存在する」テストを維持する。
+そのうえで、次の内容を設定カタログのテストに追加する。
+
+- 6グループが設計どおりの順序で現れる。
+- 各設定が設計どおりのグループに所属する。
+- 各グループの項目が設計どおりの順序で並ぶ。
+- 同じグループが離れた位置に再登場しない。
+
+README は実行時データではないため、テストから解析しない。
+実装レビューでは、設定カタログと README の見出し、所属項目、順序を差分上で照合する。
+
+## 互換性
+
+保存済み設定はキーと値をそのまま利用できる。
+設定移行処理やバージョン判定は不要である。
+
+## 完了条件
+
+- 設定画面に6グループが設計どおりの順序で表示される。
+- 28項目が欠落や重複なく設計どおりのグループに表示される。
+- README の Configuration が同じグループ構成と項目順を持つ。
+- README の Configuration が28個の保存設定だけを列挙する。
+- README に未掲載だった3項目が追加される。
+- 設定値と実行時動作が変更されない。
+- 設定カタログのテスト、全テスト、型検査、lint が通る。

esbuild.config.mjs

@@ -1,6 +1,6 @@
 import esbuild from "esbuild"
+import { builtinModules } from "node:module"
 import process from "process"
-import builtins from "builtin-modules"
 
 const banner = `/*
 THIS IS A GENERATED/BUNDLED FILE BY ESBUILD
@@ -30,7 +30,7 @@ const context = await esbuild.context({
         "@lezer/common",
         "@lezer/highlight",
         "@lezer/lr",
-        ...builtins,
+        ...builtinModules,
     ],
     format: "cjs",
     target: "esnext",

manifest.json

@@ -1,9 +1,9 @@
 {
 	"id": "automatic-linker",
 	"name": "Automatic Linker",
-	"version": "4.0.0",
+	"version": "4.7.2",
 	"minAppVersion": "1.9.0",
-	"description": "Automatically converts plain text file references into wiki links (i.e. `[[...]]`)",
+	"description": "Automatically converts plain text file references into wiki links (i.e. `[[...]]`).",
 	"author": "Kodai Nakamura",
 	"isDesktopOnly": false
 }

obsidian-ext.d.ts

@@ -7,7 +7,7 @@ declare module "obsidian" {
             commands: {
                 "editor:save-file": {
                     callback?: () => void
-                    checkCallback?: (checking: boolean) => void
+                    checkCallback?: (checking: boolean) => boolean | void
                 }
             }
         }

package.json

@@ -1,6 +1,6 @@
 {
 	"name": "automatic-linker",
-	"version": "4.0.0",
+	"version": "4.7.2",
 	"description": "Automatically converts plain text file references into Obsidian wiki links (i.e. `[[...]]`)",
 	"main": "main.js",
 	"scripts": {
@@ -12,6 +12,7 @@
 		"tsc": "tsc -noEmit -skipLibCheck",
 		"tsc:watch": "tsc -noEmit -skipLibCheck --watch",
 		"lint": "eslint .",
+		"lint:fix": "eslint . --fix",
 		"lint:watch": "nodemon --watch src --ext js,ts --exec \"npm run lint\""
 	},
 	"keywords": [],
@@ -24,14 +25,12 @@
 		"@types/node": "^22.12.0",
 		"@typescript-eslint/eslint-plugin": "^8.18.2",
 		"@typescript-eslint/parser": "^8.18.2",
-		"builtin-modules": "3.3.0",
 		"esbuild": "0.17.3",
 		"eslint": "^9.17.0",
 		"globals": "^16.5.0",
 		"nodemon": "^3.1.11",
 		"obsidian": "latest",
 		"obsidian-typings": "^2.15.0",
-		"prettier": "^3.5.1",
 		"tslib": "2.4.0",
 		"typescript": "^5.7.2",
 		"typescript-eslint": "^8.18.2",
@@ -42,6 +41,7 @@
 	},
 	"dependencies": {
 		"@codemirror/state": "6.5.0",
+		"@codemirror/view": "^6.38.6",
 		"@types/async-lock": "^1.4.2",
 		"async-lock": "^1.4.1",
 		"diff-match-patch": "^1.0.5"

pnpm-lock.yaml

@@ -11,6 +11,9 @@ importers:
       '@codemirror/state':
         specifier: 6.5.0
         version: 6.5.0
+      '@codemirror/view':
+        specifier: ^6.38.6
+        version: 6.43.0
       '@types/async-lock':
         specifier: ^1.4.2
         version: 1.4.2
@@ -39,9 +42,6 @@ importers:
       '@typescript-eslint/parser':
         specifier: ^8.18.2
         version: 8.50.0(eslint@9.39.2)(typescript@5.9.3)
-      builtin-modules:
-        specifier: 3.3.0
-        version: 3.3.0
       esbuild:
         specifier: 0.17.3
         version: 0.17.3
@@ -56,13 +56,10 @@ importers:
         version: 3.1.11
       obsidian:
         specifier: latest
-        version: 1.8.7(@codemirror/state@6.5.0)(@codemirror/view@6.36.7)
+        version: 1.8.7(@codemirror/state@6.5.0)(@codemirror/view@6.43.0)
       obsidian-typings:
         specifier: ^2.15.0
-        version: 2.44.3(@codemirror/view@6.36.7)(@pixi/core@7.2.4)(@pixi/display@7.2.4(@pixi/core@7.2.4))(@pixi/utils@7.2.4)
-      prettier:
-        specifier: ^3.5.1
-        version: 3.5.3
+        version: 2.44.3(@codemirror/view@6.43.0)(@pixi/core@7.2.4)(@pixi/display@7.2.4(@pixi/core@7.2.4))(@pixi/utils@7.2.4)
       tslib:
         specifier: 2.4.0
         version: 2.4.0
@@ -119,8 +116,11 @@ packages:
   '@codemirror/state@6.5.0':
     resolution: {integrity: sha512-MwBHVK60IiIHDcoMet78lxt6iw5gJOGSbNbOIVBHWVXIH4/Nq1+GQgLLGgI1KlnN86WDXsPudVaqYHKBIx7Eyw==}
 
-  '@codemirror/view@6.36.7':
-    resolution: {integrity: sha512-kCWGW/chWGPgZqfZ36Um9Iz0X2IVpmCjg1P/qY6B6a2ecXtWRRAigmpJ6YgUQ5lTWXMyyVdfmpzhLZmsZQMbtg==}
+  '@codemirror/state@6.6.0':
+    resolution: {integrity: sha512-4nbvra5R5EtiCzr9BTHiTLc+MLXK2QGiAVYMyi8PkQd3SR+6ixar/Q/01Fa21TBIDOZXgeWV4WppsQolSreAPQ==}
+
+  '@codemirror/view@6.43.0':
+    resolution: {integrity: sha512-V7ZCLQO3Jus9hzh2jVCCPW3mO4IBMr43O37PqSUYautJSnnJF41YlgLw21x0fLJTYvJ+Vkm6Gp+qKGH9pltgXA==}
 
   '@electron/get@2.0.3':
     resolution: {integrity: sha512-Qkzpg2s9GnVV2I2BjRksUi43U5e6+zaQMcjoJy0C+C5oxaKl+fmckGDQFtRpZpZV0NQekuZZ+tGz7EA9TVnQtQ==}
@@ -512,30 +512,35 @@ packages:
     engines: {node: '>= 10'}
     cpu: [arm64]
     os: [linux]
+    libc: [glibc]
 
   '@napi-rs/canvas-linux-arm64-musl@0.1.70':
     resolution: {integrity: sha512-wBTOllEYNfJCHOdZj9v8gLzZ4oY3oyPX8MSRvaxPm/s7RfEXxCyZ8OhJ5xAyicsDdbE5YBZqdmaaeP5+xKxvtg==}
     engines: {node: '>= 10'}
     cpu: [arm64]
     os: [linux]
+    libc: [musl]
 
   '@napi-rs/canvas-linux-riscv64-gnu@0.1.70':
     resolution: {integrity: sha512-GVUUPC8TuuFqHip0rxHkUqArQnlzmlXmTEBuXAWdgCv85zTCFH8nOHk/YCF5yo0Z2eOm8nOi90aWs0leJ4OE5Q==}
     engines: {node: '>= 10'}
     cpu: [riscv64]
     os: [linux]
+    libc: [glibc]
 
   '@napi-rs/canvas-linux-x64-gnu@0.1.70':
     resolution: {integrity: sha512-/kvUa2lZRwGNyfznSn5t1ShWJnr/m5acSlhTV3eXECafObjl0VBuA1HJw0QrilLpb4Fe0VLywkpD1NsMoVDROQ==}
     engines: {node: '>= 10'}
     cpu: [x64]
     os: [linux]
+    libc: [glibc]
 
   '@napi-rs/canvas-linux-x64-musl@0.1.70':
     resolution: {integrity: sha512-aqlv8MLpycoMKRmds7JWCfVwNf1fiZxaU7JwJs9/ExjTD8lX2KjsO7CTeAj5Cl4aEuzxUWbJPUUE2Qu9cZ1vfg==}
     engines: {node: '>= 10'}
     cpu: [x64]
     os: [linux]
+    libc: [musl]
 
   '@napi-rs/canvas-win32-x64-msvc@0.1.70':
     resolution: {integrity: sha512-Q9QU3WIpwBTVHk4cPfBjGHGU4U0llQYRXgJtFtYqqGNEOKVN4OT6PQ+ve63xwIPODMpZ0HHyj/KLGc9CWc3EtQ==}
@@ -779,61 +784,73 @@ packages:
     resolution: {integrity: sha512-de6TFZYIvJwRNjmW3+gaXiZ2DaWL5D5yGmSYzkdzjBDS3W+B9JQ48oZEsmMvemqjtAFzE16DIBLqd6IQQRuG9Q==}
     cpu: [arm]
     os: [linux]
+    libc: [glibc]
 
   '@rollup/rollup-linux-arm-musleabihf@4.40.2':
     resolution: {integrity: sha512-urjaEZubdIkacKc930hUDOfQPysezKla/O9qV+O89enqsqUmQm8Xj8O/vh0gHg4LYfv7Y7UsE3QjzLQzDYN1qg==}
     cpu: [arm]
     os: [linux]
+    libc: [musl]
 
   '@rollup/rollup-linux-arm64-gnu@4.40.2':
     resolution: {integrity: sha512-KlE8IC0HFOC33taNt1zR8qNlBYHj31qGT1UqWqtvR/+NuCVhfufAq9fxO8BMFC22Wu0rxOwGVWxtCMvZVLmhQg==}
     cpu: [arm64]
     os: [linux]
+    libc: [glibc]
 
   '@rollup/rollup-linux-arm64-musl@4.40.2':
     resolution: {integrity: sha512-j8CgxvfM0kbnhu4XgjnCWJQyyBOeBI1Zq91Z850aUddUmPeQvuAy6OiMdPS46gNFgy8gN1xkYyLgwLYZG3rBOg==}
     cpu: [arm64]
     os: [linux]
+    libc: [musl]
 
   '@rollup/rollup-linux-loongarch64-gnu@4.40.2':
     resolution: {integrity: sha512-Ybc/1qUampKuRF4tQXc7G7QY9YRyeVSykfK36Y5Qc5dmrIxwFhrOzqaVTNoZygqZ1ZieSWTibfFhQ5qK8jpWxw==}
     cpu: [loong64]
     os: [linux]
+    libc: [glibc]
 
   '@rollup/rollup-linux-powerpc64le-gnu@4.40.2':
     resolution: {integrity: sha512-3FCIrnrt03CCsZqSYAOW/k9n625pjpuMzVfeI+ZBUSDT3MVIFDSPfSUgIl9FqUftxcUXInvFah79hE1c9abD+Q==}
     cpu: [ppc64]
     os: [linux]
+    libc: [glibc]
 
   '@rollup/rollup-linux-riscv64-gnu@4.40.2':
     resolution: {integrity: sha512-QNU7BFHEvHMp2ESSY3SozIkBPaPBDTsfVNGx3Xhv+TdvWXFGOSH2NJvhD1zKAT6AyuuErJgbdvaJhYVhVqrWTg==}
     cpu: [riscv64]
     os: [linux]
+    libc: [glibc]
 
   '@rollup/rollup-linux-riscv64-musl@4.40.2':
     resolution: {integrity: sha512-5W6vNYkhgfh7URiXTO1E9a0cy4fSgfE4+Hl5agb/U1sa0kjOLMLC1wObxwKxecE17j0URxuTrYZZME4/VH57Hg==}
     cpu: [riscv64]
     os: [linux]
+    libc: [musl]
 
   '@rollup/rollup-linux-s390x-gnu@4.40.2':
     resolution: {integrity: sha512-B7LKIz+0+p348JoAL4X/YxGx9zOx3sR+o6Hj15Y3aaApNfAshK8+mWZEf759DXfRLeL2vg5LYJBB7DdcleYCoQ==}
     cpu: [s390x]
     os: [linux]
+    libc: [glibc]
 
   '@rollup/rollup-linux-x64-gnu@4.40.2':
     resolution: {integrity: sha512-lG7Xa+BmBNwpjmVUbmyKxdQJ3Q6whHjMjzQplOs5Z+Gj7mxPtWakGHqzMqNER68G67kmCX9qX57aRsW5V0VOng==}
     cpu: [x64]
     os: [linux]
+    libc: [glibc]
 
   '@rollup/rollup-linux-x64-gnu@4.6.1':
     resolution: {integrity: sha512-DNGZvZDO5YF7jN5fX8ZqmGLjZEXIJRdJEdTFMhiyXqyXubBa0WVLDWSNlQ5JR2PNgDbEV1VQowhVRUh+74D+RA==}
     cpu: [x64]
     os: [linux]
+    libc: [glibc]
 
   '@rollup/rollup-linux-x64-musl@4.40.2':
     resolution: {integrity: sha512-tD46wKHd+KJvsmije4bUskNuvWKFcTOIM9tZ/RrmIvcXnbi0YK/cKS9FzFtAm7Oxi2EhV5N2OpfFB348vSQRXA==}
     cpu: [x64]
     os: [linux]
+    libc: [musl]
 
   '@rollup/rollup-win32-arm64-msvc@4.40.2':
     resolution: {integrity: sha512-Bjv/HG8RRWLNkXwQQemdsWw4Mg+IJ29LK+bJPW2SCzPKOUaMmPEppQlu/Fqk1d7+DX3V7JbFdbkh/NMmurT6Pg==}
@@ -1168,10 +1185,6 @@ packages:
   buffer-crc32@0.2.13:
     resolution: {integrity: sha512-VO9Ht/+p3SN7SKWqcrgEzjGbRSJYTx+Q1pTQC0wrWqHx0vpJraQ6GtHx8tvcg1rlK1byhU5gccxgOgj7B0TDkQ==}
 
-  builtin-modules@3.3.0:
-    resolution: {integrity: sha512-zhaCDicdLuWN5UbN5IMnFqNMhNfo919sH85y2/ea+5Yg9TsTkeZxpL+JLbp6cgYFS4sRLp3YV4S6yDuqVWHYOw==}
-    engines: {node: '>=6'}
-
   cac@6.7.14:
     resolution: {integrity: sha512-b6Ilus+c3RrdDk+JhLKUAQfzzgLEPy6wcXqS7f/xe1EETvsDP6GORG7SFuOs6cID5YkqchW/LXZbX5bc8j7ZcQ==}
     engines: {node: '>=8'}
@@ -2012,11 +2025,6 @@ packages:
     resolution: {integrity: sha512-vkcDPrRZo1QZLbn5RLGPpg/WmIQ65qoWWhcGKf/b5eplkkarX0m9z8ppCat4mlOqUsWpyNuYgO3VRyrYHSzX5g==}
     engines: {node: '>= 0.8.0'}
 
-  prettier@3.5.3:
-    resolution: {integrity: sha512-QQtaxnoDJeAkDvDKWCLiwIXkTgRhwYDEQCghU9Z6q03iyek/rxRh/2lC3HB7P8sWT2xC/y5JDctPLBIGzHKbhw==}
-    engines: {node: '>=14'}
-    hasBin: true
-
   progress@2.0.3:
     resolution: {integrity: sha512-7PiHtLll5LdnKIMw100I+8xJXR5gW2QwWYkT6iJva0bXitZKa/XMrSbdmg3r2Xnaidz9Qumd0VPaMrZlF9V9sA==}
     engines: {node: '>=0.4.0'}
@@ -2416,16 +2424,21 @@ snapshots:
   '@codemirror/search@6.5.10':
     dependencies:
       '@codemirror/state': 6.5.0
-      '@codemirror/view': 6.36.7
+      '@codemirror/view': 6.43.0
       crelt: 1.0.6
 
   '@codemirror/state@6.5.0':
     dependencies:
       '@marijn/find-cluster-break': 1.0.2
 
-  '@codemirror/view@6.36.7':
+  '@codemirror/state@6.6.0':
     dependencies:
-      '@codemirror/state': 6.5.0
+      '@marijn/find-cluster-break': 1.0.2
+
+  '@codemirror/view@6.43.0':
+    dependencies:
+      '@codemirror/state': 6.6.0
+      crelt: 1.0.6
       style-mod: 4.1.2
       w3c-keyname: 2.2.8
 
@@ -3345,8 +3358,6 @@ snapshots:
 
   buffer-crc32@0.2.13: {}
 
-  builtin-modules@3.3.0: {}
-
   cac@6.7.14: {}
 
   cacheable-lookup@5.0.4: {}
@@ -4194,7 +4205,7 @@ snapshots:
   object-keys@1.1.1:
     optional: true
 
-  obsidian-typings@2.44.3(@codemirror/view@6.36.7)(@pixi/core@7.2.4)(@pixi/display@7.2.4(@pixi/core@7.2.4))(@pixi/utils@7.2.4):
+  obsidian-typings@2.44.3(@codemirror/view@6.43.0)(@pixi/core@7.2.4)(@pixi/display@7.2.4(@pixi/core@7.2.4))(@pixi/utils@7.2.4):
     dependencies:
       '@capacitor/core': 6.2.1
       '@codemirror/search': 6.5.10
@@ -4212,7 +4223,7 @@ snapshots:
       i18next: 23.16.8
       mermaid: 11.6.0
       moment: 2.30.1
-      obsidian: 1.8.7(@codemirror/state@6.5.0)(@codemirror/view@6.36.7)
+      obsidian: 1.8.7(@codemirror/state@6.5.0)(@codemirror/view@6.43.0)
       pdfjs-dist: 5.2.133
       pixi.js: 7.2.4(@pixi/utils@7.2.4)
       scrypt-js: 3.0.1
@@ -4224,10 +4235,10 @@ snapshots:
       - '@pixi/utils'
       - supports-color
 
-  obsidian@1.8.7(@codemirror/state@6.5.0)(@codemirror/view@6.36.7):
+  obsidian@1.8.7(@codemirror/state@6.5.0)(@codemirror/view@6.43.0):
     dependencies:
       '@codemirror/state': 6.5.0
-      '@codemirror/view': 6.36.7
+      '@codemirror/view': 6.43.0
       '@types/codemirror': 5.60.8
       moment: 2.29.4
 
@@ -4346,8 +4357,6 @@ snapshots:
 
   prelude-ls@1.2.1: {}
 
-  prettier@3.5.3: {}
-
   progress@2.0.3: {}
 
   pstree.remy@1.1.8: {}

src/__mocks__/obsidian.ts

@@ -0,0 +1,6 @@
+export const request = async () => ({})
+export class Notice {
+    constructor() {}
+    hide() {}
+    setMessage() {}
+}

src/__tests__/formatting-run.test.ts

@@ -0,0 +1,208 @@
+import { describe, expect, it } from "vitest"
+import {
+    formatMarkdownBody,
+    formatMarkdownDocument,
+    formatMarkdownSelection,
+    toReplaceLinksSettings,
+} from "../formatting-run"
+import { buildCandidateTrieForTest } from "../replace-links/__tests__/test-helpers"
+import { DEFAULT_SETTINGS } from "../settings/settings-info"
+
+describe("toReplaceLinksSettings", () => {
+    it("projects only replacement settings and applies baseDir", () => {
+        expect(toReplaceLinksSettings({
+            ...DEFAULT_SETTINGS,
+            proximityBasedLinking: false,
+            ignoreDateFormats: false,
+            ignoreCase: false,
+            matchSentenceCase: false,
+            preventSelfLinking: true,
+            removeAliasInDirs: ["archive"],
+            ignoreHeadings: true,
+            ignoreMarkdownTables: true,
+        }, "pages")).toEqual({
+            proximityBasedLinking: false,
+            baseDir: "pages",
+            ignoreDateFormats: false,
+            ignoreCase: false,
+            matchSentenceCase: false,
+            preventSelfLinking: true,
+            removeAliasInDirs: ["archive"],
+            ignoreHeadings: true,
+            ignoreMarkdownTables: true,
+        })
+    })
+})
+
+describe("formatMarkdownDocument", () => {
+    it("preserves frontmatter and respects URL title opt-out", () => {
+        const result = formatMarkdownDocument({
+            content: "---\nautomatic-linker-disable-url-title: true\n---\nhttps://example.com",
+            filePath: "current-file.md",
+            frontmatter: { "automatic-linker-disable-url-title": true },
+            settings: {
+                ...DEFAULT_SETTINGS,
+                formatGitHubURLs: false,
+                formatJiraURLs: false,
+                formatLinearURLs: false,
+                replaceUrlWithTitle: true,
+            },
+            urlTitleMap: new Map([["https://example.com", "Example Title"]]),
+        })
+
+        expect(result).toBe(
+            "---\nautomatic-linker-disable-url-title: true\n---\nhttps://example.com",
+        )
+    })
+
+    it("formats GitHub URLs in frontmatter without moving body-only formatting into frontmatter", () => {
+        const { candidateMap, trie } = buildCandidateTrieForTest({
+            files: [{ path: "notes/TypeScript" }],
+            settings: {
+                scoped: false,
+                baseDir: undefined,
+                ignoreCase: true,
+            },
+        })
+
+        const result = formatMarkdownDocument({
+            content:
+                "---\nautomatic-linker-disable-url-title: true\nreference: https://github.com/openai/openai/issues/1\nterm: TypeScript\n---\nTypeScript https://example.com",
+            filePath: "current-file.md",
+            frontmatter: {
+                "automatic-linker-disable-url-title": true,
+            },
+            settings: {
+                ...DEFAULT_SETTINGS,
+                formatGitHubURLs: true,
+                formatJiraURLs: false,
+                formatLinearURLs: false,
+                replaceUrlWithTitle: true,
+                ignoreCase: true,
+            },
+            candidateIndex: { candidateMap, trie },
+        })
+
+        expect(result).toBe(
+            "---\nautomatic-linker-disable-url-title: true\nreference: [[github/openai/openai/issues/1]] [🔗](https://github.com/openai/openai/issues/1)\nterm: TypeScript\n---\n[[notes/TypeScript|TypeScript]] https://example.com",
+        )
+    })
+
+    it("runs URL formatting, URL titles, and link replacement in order", () => {
+        const { candidateMap, trie } = buildCandidateTrieForTest({
+            files: [{ path: "notes/TypeScript" }],
+            settings: {
+                scoped: false,
+                baseDir: undefined,
+                ignoreCase: true,
+            },
+        })
+
+        const result = formatMarkdownDocument({
+            content: "Read TypeScript at https://example.com",
+            filePath: "current-file.md",
+            settings: {
+                ...DEFAULT_SETTINGS,
+                formatGitHubURLs: false,
+                formatJiraURLs: false,
+                formatLinearURLs: false,
+                replaceUrlWithTitle: true,
+                ignoreCase: true,
+            },
+            candidateIndex: { candidateMap, trie },
+            urlTitleMap: new Map([["https://example.com", "Example Title"]]),
+        })
+
+        expect(result).toBe("Read [[notes/TypeScript|TypeScript]] at [Example Title](https://example.com)")
+    })
+})
+
+describe("formatMarkdownBody", () => {
+    it("formats selected body text without frontmatter splitting", () => {
+        const { candidateMap, trie } = buildCandidateTrieForTest({
+            files: [{ path: "notes/TypeScript" }],
+            settings: {
+                scoped: false,
+                baseDir: undefined,
+                ignoreCase: true,
+            },
+        })
+
+        const result = formatMarkdownBody({
+            body: "TypeScript",
+            filePath: "current-file.md",
+            settings: {
+                ...DEFAULT_SETTINGS,
+                formatGitHubURLs: false,
+                formatJiraURLs: false,
+                formatLinearURLs: false,
+                replaceUrlWithTitle: false,
+                ignoreCase: true,
+            },
+            candidateIndex: { candidateMap, trie },
+        })
+
+        expect(result).toBe("[[notes/TypeScript|TypeScript]]")
+    })
+})
+
+describe("formatMarkdownSelection", () => {
+    it("keeps selection formatting to link replacement only", () => {
+        const { candidateMap, trie } = buildCandidateTrieForTest({
+            files: [{ path: "notes/TypeScript" }],
+            settings: {
+                scoped: false,
+                baseDir: undefined,
+                ignoreCase: true,
+            },
+        })
+
+        const result = formatMarkdownSelection({
+            body: "TypeScript https://github.com/openai/openai/issues/1",
+            filePath: "current-file.md",
+            settings: {
+                ...DEFAULT_SETTINGS,
+                formatGitHubURLs: true,
+                formatJiraURLs: true,
+                formatLinearURLs: true,
+                replaceUrlWithTitle: true,
+                ignoreCase: true,
+            },
+            candidateIndex: { candidateMap, trie },
+        })
+
+        expect(result).toBe(
+            "[[notes/TypeScript|TypeScript]] https://github.com/openai/openai/issues/1",
+        )
+    })
+
+    it("leaves linear URLs unchanged when a linear note exists", () => {
+        const { candidateMap, trie } = buildCandidateTrieForTest({
+            files: [
+                { path: "notes/linear" },
+                { path: "notes/TypeScript" },
+            ],
+            settings: {
+                scoped: false,
+                baseDir: undefined,
+                ignoreCase: true,
+            },
+        })
+
+        const result = formatMarkdownSelection({
+            body: "linear://workspace/issue/ACME-123",
+            filePath: "current-file.md",
+            settings: {
+                ...DEFAULT_SETTINGS,
+                formatGitHubURLs: true,
+                formatJiraURLs: true,
+                formatLinearURLs: true,
+                replaceUrlWithTitle: true,
+                ignoreCase: true,
+            },
+            candidateIndex: { candidateMap, trie },
+        })
+
+        expect(result).toBe("linear://workspace/issue/ACME-123")
+    })
+})

src/__tests__/frontmatter-utils.test.ts

@@ -0,0 +1,14 @@
+import { describe, expect, it } from "vitest"
+import { isUrlTitleReplacementOff } from "../frontmatter-utils"
+
+describe("frontmatter utils", () => {
+    it("detects URL title replacement opt-out", () => {
+        expect(isUrlTitleReplacementOff({
+            "automatic-linker-disable-url-title": true,
+        })).toBe(true)
+    })
+
+    it("does not disable URL title replacement when the opt-out is absent", () => {
+        expect(isUrlTitleReplacementOff(undefined)).toBe(false)
+    })
+})

src/__tests__/main-link-generator.test.ts

@@ -0,0 +1,131 @@
+import { describe, expect, it, vi } from "vitest"
+import { buildCandidateTrieForTest } from "../replace-links/__tests__/test-helpers"
+import { DEFAULT_SETTINGS } from "../settings/settings-info"
+
+class MockTFile {
+    path: string
+
+    constructor(path: string) {
+        this.path = path
+    }
+}
+
+vi.mock("obsidian", () => ({
+    App: class {},
+    Editor: class {},
+    getFrontMatterInfo: () => ({ contentStart: 0 }),
+    MarkdownView: class {},
+    Notice: class {},
+    parseFrontMatterAliases: () => [],
+    Plugin: class {
+        app: unknown
+
+        constructor(app: unknown) {
+            this.app = app
+        }
+    },
+    PluginSettingTab: class {},
+    request: async () => ({}),
+    Setting: class {
+        setName() { return this }
+        setDesc() { return this }
+        setHeading() { return this }
+        addToggle() { return this }
+        addTextArea() { return this }
+    },
+    TFile: MockTFile,
+}))
+
+describe("AutomaticLinkerPlugin link generator", () => {
+    it("escapes alias separators generated by Obsidian inside markdown tables", async () => {
+        const { default: AutomaticLinkerPlugin } = await import("../main")
+        const settings = {
+            scoped: false,
+            baseDir: undefined,
+            ignoreCase: true,
+        }
+        const { candidateMap, trie } = buildCandidateTrieForTest({
+            files: [{ path: "notes/foo", aliases: ["bar"] }],
+            settings,
+        })
+        const targetFile = new MockTFile("notes/foo.md")
+        const app = {
+            fileManager: {
+                generateMarkdownLink: vi.fn(() => "[[notes/foo|bar]]"),
+            },
+            vault: {
+                getAbstractFileByPath: vi.fn((path: string) => {
+                    if (path === "notes/foo.md") return targetFile
+                    return null
+                }),
+                getConfig: vi.fn(),
+            },
+        }
+        const plugin = new AutomaticLinkerPlugin(app as never, {} as never)
+        plugin.settings = {
+            ...DEFAULT_SETTINGS,
+            formatGitHubURLs: false,
+            formatJiraURLs: false,
+            replaceUrlWithTitle: false,
+            respectNewFileFolderPath: false,
+        }
+        ;(plugin as unknown as { trie: typeof trie }).trie = trie
+        ;(plugin as unknown as { candidateMap: typeof candidateMap }).candidateMap = candidateMap
+
+        const result = plugin.modifyLinks("| bar | x |\n| --- | --- |\n", "current-file.md")
+
+        expect(result).toBe("| [[notes/foo\\|bar]] | x |\n| --- | --- |\n")
+    })
+
+    it("keeps selection formatting to link replacement only", async () => {
+        const { default: AutomaticLinkerPlugin } = await import("../main")
+        const settings = {
+            scoped: false,
+            baseDir: undefined,
+            ignoreCase: true,
+        }
+        const { candidateMap, trie } = buildCandidateTrieForTest({
+            files: [{ path: "notes/TypeScript" }],
+            settings,
+        })
+        const replaceSelection = vi.fn()
+        const app = {
+            workspace: {
+                getActiveFile: vi.fn(() => ({ path: "current-file.md" })),
+                activeEditor: {
+                    editor: {
+                        getSelection: vi.fn(() => "TypeScript https://github.com/openai/openai/issues/1"),
+                        replaceSelection,
+                    },
+                },
+            },
+            vault: {
+                getConfig: vi.fn(() => "pages"),
+                getAbstractFileByPath: vi.fn((path: string) => {
+                    if (path === "notes/TypeScript.md") return { path: "notes/TypeScript.md" }
+                    return null
+                }),
+            },
+            fileManager: {
+                generateMarkdownLink: vi.fn(() => "[[notes/TypeScript|TypeScript]]"),
+            },
+        }
+        const plugin = new AutomaticLinkerPlugin(app as never, {} as never)
+        plugin.settings = {
+            ...DEFAULT_SETTINGS,
+            formatGitHubURLs: true,
+            formatJiraURLs: true,
+            formatLinearURLs: true,
+            replaceUrlWithTitle: true,
+            respectNewFileFolderPath: true,
+        }
+        ;(plugin as unknown as { trie: typeof trie }).trie = trie
+        ;(plugin as unknown as { candidateMap: typeof candidateMap }).candidateMap = candidateMap
+
+        await plugin.mofifyLinksSelection()
+
+        expect(replaceSelection).toHaveBeenCalledWith(
+            "[[notes/TypeScript|TypeScript]] https://github.com/openai/openai/issues/1",
+        )
+    })
+})

src/__tests__/main-url-title-frontmatter.test.ts

@@ -0,0 +1,79 @@
+import { afterEach, describe, expect, it, vi } from "vitest"
+import { DEFAULT_SETTINGS } from "../settings/settings-info"
+
+const requestMock = vi.hoisted(() => vi.fn())
+
+class MockTFile {
+    path: string
+
+    constructor(path: string) {
+        this.path = path
+    }
+}
+
+vi.mock("obsidian", () => ({
+    App: class {},
+    Editor: class {},
+    getFrontMatterInfo: (content: string) => {
+        const frontmatter = content.match(/^---\n[\s\S]*?\n---\n?/)
+        return { contentStart: frontmatter?.[0].length ?? 0 }
+    },
+    MarkdownView: class {},
+    Notice: class {},
+    parseFrontMatterAliases: () => [],
+    Plugin: class {
+        app: unknown
+
+        constructor(app: unknown) {
+            this.app = app
+        }
+    },
+    PluginSettingTab: class {},
+    request: requestMock,
+    Setting: class {
+        setName() { return this }
+        setDesc() { return this }
+        setHeading() { return this }
+        addToggle() { return this }
+        addTextArea() { return this }
+        addText() { return this }
+    },
+    TFile: MockTFile,
+}))
+
+describe("AutomaticLinkerPlugin URL title frontmatter opt-out", () => {
+    afterEach(() => {
+        requestMock.mockReset()
+    })
+
+    it("does not fetch URL titles when disabled in active file frontmatter", async () => {
+        const { default: AutomaticLinkerPlugin } = await import("../main")
+        const activeFile = new MockTFile("current-file.md")
+        const app = {
+            metadataCache: {
+                getFileCache: vi.fn(() => ({
+                    frontmatter: {
+                        "automatic-linker-disable-url-title": true,
+                    },
+                })),
+            },
+            vault: {
+                read: vi.fn(async () => (
+                    "---\nautomatic-linker-disable-url-title: true\n---\nhttps://example.com"
+                )),
+            },
+            workspace: {
+                getActiveFile: vi.fn(() => activeFile),
+            },
+        }
+        const plugin = new AutomaticLinkerPlugin(app as never, {} as never)
+        plugin.settings = {
+            ...DEFAULT_SETTINGS,
+            replaceUrlWithTitle: true,
+        }
+
+        await plugin.buildUrlTitleMap()
+
+        expect(requestMock).not.toHaveBeenCalled()
+    })
+})

src/__tests__/markdown-segments.test.ts

@@ -0,0 +1,102 @@
+import { describe, expect, it } from "vitest"
+import { mapMarkdownProse, segmentMarkdown } from "../markdown-segments"
+
+describe("segmentMarkdown", () => {
+    it("round-trips prose and protected inline code", () => {
+        const text = "Use `TypeScript` with TypeScript"
+        const segments = segmentMarkdown(text)
+
+        expect(segments.map(segment => ({
+            kind: segment.kind,
+            protectedKind: segment.protectedKind,
+            text: segment.text,
+        }))).toEqual([
+            { kind: "prose", protectedKind: undefined, text: "Use " },
+            { kind: "protected", protectedKind: "inline-code", text: "`TypeScript`" },
+            { kind: "prose", protectedKind: undefined, text: " with TypeScript" },
+        ])
+        expect(segments.map(segment => segment.text).join("")).toBe(text)
+    })
+
+    it("protects fenced code blocks including unclosed blocks", () => {
+        const text = "before\n```ts\nTypeScript"
+        const segments = segmentMarkdown(text)
+
+        expect(segments.map(segment => ({
+            kind: segment.kind,
+            protectedKind: segment.protectedKind,
+            text: segment.text,
+        }))).toEqual([
+            { kind: "prose", protectedKind: undefined, text: "before\n" },
+            { kind: "protected", protectedKind: "fenced-code", text: "```ts\nTypeScript" },
+        ])
+    })
+
+    it("protects tilde fenced code blocks", () => {
+        const text = "before\n~~~ts\nTypeScript\n~~~\nafter"
+        const segments = segmentMarkdown(text)
+
+        expect(segments.map(segment => ({
+            kind: segment.kind,
+            protectedKind: segment.protectedKind,
+            text: segment.text,
+        }))).toEqual([
+            { kind: "prose", protectedKind: undefined, text: "before\n" },
+            { kind: "protected", protectedKind: "fenced-code", text: "~~~ts\nTypeScript\n~~~\n" },
+            { kind: "prose", protectedKind: undefined, text: "after" },
+        ])
+    })
+
+    it("protects headings, tables, and callouts when requested", () => {
+        const text = "# TypeScript\n| TypeScript |\n> [!note]\n> TypeScript\nTypeScript"
+        const segments = segmentMarkdown(text, {
+            protectHeadings: true,
+            protectTableRows: true,
+            protectCallouts: true,
+        })
+
+        expect(segments.filter(segment => segment.kind === "protected").map(segment => segment.protectedKind)).toEqual([
+            "heading",
+            "table-row",
+            "callout",
+        ])
+        expect(segments.map(segment => segment.text).join("")).toBe(text)
+    })
+
+    it("protects linear URLs when requested", () => {
+        const text = "linear://workspace/issue/ACME-123"
+        const segments = segmentMarkdown(text, {
+            protectUrls: true,
+        })
+
+        expect(segments).toEqual([
+            {
+                kind: "protected",
+                protectedKind: "url",
+                start: 0,
+                end: text.length,
+                text,
+            },
+        ])
+    })
+})
+
+describe("mapMarkdownProse", () => {
+    it("transforms only prose segments", () => {
+        const result = mapMarkdownProse(
+            "TypeScript `TypeScript` [[TypeScript]]",
+            text => text.replace(/TypeScript/g, "TS"),
+        )
+
+        expect(result).toBe("TS `TypeScript` [[TypeScript]]")
+    })
+
+    it("does not globally protect angle-bracket autolinks", () => {
+        const result = mapMarkdownProse(
+            "<https://example.com> https://example.com",
+            text => text.replace(/https:\/\/example\.com/g, "URL"),
+        )
+
+        expect(result).toBe("<URL> URL")
+    })
+})

src/__tests__/plugin-compat.test.ts

@@ -0,0 +1,34 @@
+import { describe, expect, it, vi } from "vitest"
+import { runAsyncSafely, sleep } from "../plugin-compat"
+
+describe("plugin-compat", () => {
+    it("sleep uses the provided scheduler", async () => {
+        let capturedDelay: number | null = null
+        const scheduledCallbacks: Array<() => void> = []
+
+        const promise = sleep(25, (callback, delay) => {
+            capturedDelay = delay
+            scheduledCallbacks.push(callback)
+            return 1
+        })
+
+        expect(capturedDelay).toBe(25)
+        expect(scheduledCallbacks).toHaveLength(1)
+
+        scheduledCallbacks[0]()
+
+        await expect(promise).resolves.toBeUndefined()
+    })
+
+    it("runAsyncSafely reports rejected tasks", async () => {
+        const onError = vi.fn()
+
+        runAsyncSafely(async () => {
+            throw new Error("boom")
+        }, onError)
+
+        await vi.waitFor(() => {
+            expect(onError).toHaveBeenCalledTimes(1)
+        })
+    })
+})

src/__tests__/trie.test.ts

@@ -0,0 +1,74 @@
+import { describe, expect, it } from "vitest"
+import { PathAndAliases } from "../path-and-aliases.types"
+import { buildCandidateTrie, buildTrie, getTopLevelDirectoryName } from "../trie"
+
+describe("getTopLevelDirectoryName", () => {
+    it("returns the first directory after the baseDir", () => {
+        expect(getTopLevelDirectoryName("pages/docs/file", "pages")).toBe("docs")
+        expect(getTopLevelDirectoryName("pages/home/readme", "pages")).toBe("home")
+    })
+
+    it("returns the first segment if baseDir is not found", () => {
+        expect(getTopLevelDirectoryName("docs/file")).toBe("docs")
+        expect(getTopLevelDirectoryName("home/readme")).toBe("home")
+    })
+})
+
+describe("buildTrie", () => {
+    it("builds a trie with the given words", () => {
+        const words = ["hello", "world", "hi"]
+        const trie = buildTrie(words)
+
+        expect(trie.children.has("h")).toBe(true)
+        expect(trie.children.has("w")).toBe(true)
+        expect(trie.children.get("h")?.children.has("e")).toBe(true)
+        expect(trie.children.get("h")?.children.get("i")?.candidate).toBe("hi")
+    })
+})
+
+describe("buildCandidateTrie", () => {
+    it("builds a candidate map and trie", () => {
+        const allFiles: PathAndAliases[] = [
+            {
+                path: "pages/docs/readme",
+                scoped: false,
+                aliases: ["intro"],
+            },
+            {
+                path: "pages/home/index",
+                scoped: false,
+                aliases: [],
+            },
+        ]
+
+        const { candidateMap, trie } = buildCandidateTrie(allFiles, "pages")
+
+        expect(candidateMap.has("pages/docs/readme")).toBe(true)
+        expect(candidateMap.has("docs/readme")).toBe(true)
+        expect(candidateMap.get("intro")?.candidates[0].canonical).toBe("pages/docs/readme|intro")
+        expect(trie.children.has("d")).toBe(true)
+        expect(trie.children.has("h")).toBe(true)
+    })
+
+    it("handles multiple candidates for the same word", () => {
+        const allFiles: PathAndAliases[] = [
+            {
+                path: "work/meeting",
+                scoped: false,
+                aliases: [],
+            },
+            {
+                path: "private/meeting",
+                scoped: false,
+                aliases: [],
+            },
+        ]
+
+        const { candidateMap } = buildCandidateTrie(allFiles, undefined, true)
+
+        const meetingData = candidateMap.get("meeting")
+        expect(meetingData?.candidates).toHaveLength(2)
+        expect(meetingData?.candidates.map(c => c.canonical)).toContain("work/meeting")
+        expect(meetingData?.candidates.map(c => c.canonical)).toContain("private/meeting")
+    })
+})

src/formatting-run.ts

@@ -0,0 +1,113 @@
+import { isUrlTitleReplacementOff } from "./frontmatter-utils"
+import {
+    LinkGenerator,
+    replaceLinks,
+} from "./replace-links/replace-links"
+import { replaceUrlWithTitle } from "./replace-url-with-title"
+import { formatURLsInText } from "./replace-urls/url-formatting"
+import {
+    AutomaticLinkerSettings,
+    projectReplaceLinksSettings,
+} from "./settings/settings-catalog"
+import { CandidateData, TrieNode } from "./trie"
+
+export interface CandidateIndex {
+    trie: TrieNode
+    candidateMap: Map<string, CandidateData>
+}
+
+export interface FormattingRunOptions {
+    content: string
+    filePath: string
+    contentStart?: number
+    frontmatter?: Record<string, unknown>
+    settings: AutomaticLinkerSettings
+    baseDir?: string
+    candidateIndex?: CandidateIndex
+    urlTitleMap?: Map<string, string>
+    linkGenerator?: LinkGenerator
+}
+
+export { projectReplaceLinksSettings as toReplaceLinksSettings } from "./settings/settings-catalog"
+
+const formatMarkdownURLs = (
+    text: string,
+    settings: AutomaticLinkerSettings,
+): string =>
+    formatURLsInText({
+        text,
+        settings,
+    })
+
+export const formatMarkdownBody = ({
+    body,
+    filePath,
+    frontmatter,
+    settings,
+    baseDir,
+    candidateIndex,
+    urlTitleMap = new Map(),
+    linkGenerator,
+}: Omit<FormattingRunOptions, "content"> & { body: string }): string => {
+    let updatedBody = formatMarkdownURLs(body, settings)
+
+    if (settings.replaceUrlWithTitle && !isUrlTitleReplacementOff(frontmatter)) {
+        updatedBody = replaceUrlWithTitle({ body: updatedBody, urlTitleMap })
+    }
+    if (candidateIndex) {
+        updatedBody = replaceLinks({
+            body: updatedBody,
+            linkResolverContext: {
+                filePath: filePath.replace(/\.md$/, ""),
+                trie: candidateIndex.trie,
+                candidateMap: candidateIndex.candidateMap,
+            },
+            settings: projectReplaceLinksSettings(settings, baseDir),
+            linkGenerator,
+        })
+    }
+
+    return updatedBody
+}
+
+export const formatMarkdownSelection = ({
+    body,
+    filePath,
+    settings,
+    baseDir,
+    candidateIndex,
+    linkGenerator,
+}: Omit<FormattingRunOptions, "content" | "frontmatter" | "urlTitleMap"> & { body: string }): string => {
+    if (!candidateIndex) {
+        return body
+    }
+
+    return replaceLinks({
+        body,
+        linkResolverContext: {
+            filePath: filePath.replace(/\.md$/, ""),
+            trie: candidateIndex.trie,
+            candidateMap: candidateIndex.candidateMap,
+        },
+        settings: projectReplaceLinksSettings(settings, baseDir),
+        linkGenerator,
+    })
+}
+
+const inferContentStart = (content: string): number => {
+    const frontmatter = content.match(/^---\r?\n[\s\S]*?\r?\n---\r?\n?/)
+    return frontmatter?.[0].length ?? 0
+}
+
+export const formatMarkdownDocument = ({
+    content,
+    contentStart = inferContentStart(content),
+    ...options
+}: FormattingRunOptions): string => {
+    const frontmatterText = formatMarkdownURLs(
+        content.slice(0, contentStart),
+        options.settings,
+    )
+    const body = content.slice(contentStart)
+    return frontmatterText + formatMarkdownBody({ ...options, body })
+}

src/frontmatter-utils.ts

@@ -34,3 +34,12 @@ export const isLinkingExcluded = (
         || frontmatter?.["automatic-linker-exclude"] === true
     )
 }
+
+/**
+ * Check if the file disables URL title fetching/replacement
+ */
+export const isUrlTitleReplacementOff = (
+    frontmatter: Record<string, unknown> | undefined,
+): boolean => {
+    return frontmatter?.["automatic-linker-disable-url-title"] === true
+}

src/main.ts

@@ -11,25 +11,28 @@ import {
     TFile,
 } from "obsidian"
 import { excludeLinks } from "./exclude-links"
+import {
+    formatMarkdownDocument,
+    formatMarkdownSelection,
+    toReplaceLinksSettings,
+} from "./formatting-run"
 import {
     isLinkingOff,
     isLinkingExcluded,
     isNamespaceScoped,
+    isUrlTitleReplacementOff,
 } from "./frontmatter-utils"
 import { PathAndAliases } from "./path-and-aliases.types"
 import { removeMinimalIndent } from "./remove-minimal-indent"
 import {
+    defaultLinkGenerator,
+    escapeLinkForMarkdownTable,
     LinkGenerator,
     LinkGeneratorParams,
     replaceLinks,
 } from "./replace-links/replace-links"
-import { replaceUrlWithTitle } from "./replace-url-with-title"
 import { getTitleFromHtml } from "./replace-url-with-title/utils/get-title-from-html"
 import { listupAllUrls } from "./replace-url-with-title/utils/list-up-all-urls"
-import { formatGitHubURL } from "./replace-urls/github"
-import { formatJiraURL } from "./replace-urls/jira"
-import { formatLinearURL } from "./replace-urls/linear"
-import { replaceURLs } from "./replace-urls/replace-urls"
 import { AutomaticLinkerPluginSettingsTab } from "./settings/settings"
 import {
     AutomaticLinkerSettings,
@@ -37,10 +40,8 @@ import {
 } from "./settings/settings-info"
 import { buildCandidateTrie, CandidateData, TrieNode } from "./trie"
 import { updateEditor } from "./update-editor"
-
-const sleep = (ms: number) => {
-    return new Promise(resolve => setTimeout(resolve, ms))
-}
+import { runAsyncSafely, sleep } from "./plugin-compat"
+import { resolveAmbiguities } from "./utils/resolve-ambiguities"
 
 export default class AutomaticLinkerPlugin extends Plugin {
     settings: AutomaticLinkerSettings
@@ -80,7 +81,7 @@ export default class AutomaticLinkerPlugin extends Plugin {
                 // File exists, use Obsidian's generateMarkdownLink API
                 try {
                     const link = this.app.fileManager.generateMarkdownLink(targetFile, sourcePath, "", alias || "")
-                    return link
+                    return escapeLinkForMarkdownTable(link, isInTable)
                 }
                 catch (error) {
                     // Fall back to default format if API fails
@@ -88,45 +89,24 @@ export default class AutomaticLinkerPlugin extends Plugin {
                 }
             }
 
-            // Fallback: use default wikilink format
-            let linkContent = linkPath
-            if (alias) {
-                linkContent = `${linkPath}|${alias}`
-            }
-            if (isInTable && linkContent.includes("|")) {
-                linkContent = linkContent.replace(/\|/g, "\\|")
-            }
-            return `[[${linkContent}]]`
+            return defaultLinkGenerator({ linkPath, sourcePath, alias, isInTable })
         }
     }
 
-    modifyLinks(fileContent: string, filePath: string): string {
-        if (this.settings.formatGitHubURLs) {
-            fileContent = replaceURLs(fileContent, this.settings, formatGitHubURL)
-        }
-
-        if (this.settings.formatJiraURLs) {
-            fileContent = replaceURLs(fileContent, this.settings, formatJiraURL)
-        }
-
-        if (this.settings.formatLinearURLs) {
-            fileContent = replaceURLs(
-                fileContent,
-                this.settings,
-                formatLinearURL,
-            )
-        }
-
-        if (this.settings.replaceUrlWithTitle) {
-            const { contentStart } = getFrontMatterInfo(fileContent)
-            const frontmatter = fileContent.slice(0, contentStart)
-            const body = fileContent.slice(contentStart)
-            const updatedBody = replaceUrlWithTitle({ body, urlTitleMap: this.urlTitleMap })
-            fileContent = frontmatter + updatedBody
-        }
-
+    modifyLinks(
+        fileContent: string,
+        filePath: string,
+        frontmatter?: Record<string, unknown>,
+    ): string {
         if (!this.trie || !this.candidateMap) {
-            return fileContent
+            return formatMarkdownDocument({
+                content: fileContent,
+                filePath,
+                contentStart: getFrontMatterInfo(fileContent).contentStart,
+                frontmatter,
+                settings: this.settings,
+                urlTitleMap: this.urlTitleMap,
+            })
         }
 
         if (this.settings.debug) {
@@ -136,28 +116,21 @@ export default class AutomaticLinkerPlugin extends Plugin {
             new Notice(`Automatic Linker: ${new Date().toISOString()} modifyLinks started.`)
         }
 
-        const { contentStart } = getFrontMatterInfo(fileContent)
-        const frontmatter = fileContent.slice(0, contentStart)
-        const linkGenerator = this.createLinkGenerator(filePath)
         const baseDir = this.settings.respectNewFileFolderPath ? this.app.vault.getConfig("newFileFolderPath") : undefined
-        const updatedBody = replaceLinks({
-            body: fileContent.slice(contentStart),
-            linkResolverContext: {
-                filePath: filePath.replace(/\.md$/, ""),
-                trie: this.trie,
-                candidateMap: this.candidateMap,
-            },
-            settings: {
-                proximityBasedLinking: this.settings.proximityBasedLinking,
-                baseDir,
-                ignoreDateFormats: this.settings.ignoreDateFormats,
-                ignoreCase: this.settings.ignoreCase,
-                preventSelfLinking: this.settings.preventSelfLinking,
-                removeAliasInDirs: this.settings.removeAliasInDirs,
-            },
-            linkGenerator,
+        const candidateIndex = this.trie && this.candidateMap
+            ? { trie: this.trie, candidateMap: this.candidateMap }
+            : undefined
+        fileContent = formatMarkdownDocument({
+            content: fileContent,
+            filePath,
+            contentStart: getFrontMatterInfo(fileContent).contentStart,
+            frontmatter,
+            settings: this.settings,
+            baseDir,
+            candidateIndex,
+            urlTitleMap: this.urlTitleMap,
+            linkGenerator: candidateIndex ? this.createLinkGenerator(filePath) : undefined,
         })
-        fileContent = frontmatter + updatedBody
 
         if (this.settings.debug) {
             console.log(new Date().toISOString(), "modifyLinks finished")
@@ -166,12 +139,11 @@ export default class AutomaticLinkerPlugin extends Plugin {
         return fileContent
     }
 
-    async modifyLinksForActiveFile() {
+    modifyLinksForActiveFile() {
         const activeFile = this.app.workspace.getActiveFile()
         if (!activeFile) return
 
-        const metadata
-            = this.app.metadataCache.getFileCache(activeFile)?.frontmatter
+        const metadata = this.app.metadataCache.getFileCache(activeFile)?.frontmatter
         if (isLinkingOff(metadata)) return
 
         const editor = this.getEditor()
@@ -179,7 +151,7 @@ export default class AutomaticLinkerPlugin extends Plugin {
 
         const fileContent = editor.getValue()
         const oldText = fileContent
-        const newText = this.modifyLinks(fileContent, activeFile.path)
+        const newText = this.modifyLinks(fileContent, activeFile.path, metadata)
         updateEditor(oldText, newText, editor)
     }
 
@@ -187,8 +159,9 @@ export default class AutomaticLinkerPlugin extends Plugin {
         this.refreshFileDataAndTrie()
         const allMarkdownFiles = this.app.vault.getMarkdownFiles()
         for (const file of allMarkdownFiles) {
+            const metadata = this.app.metadataCache.getFileCache(file)?.frontmatter
             await this.app.vault.process(file, (fileContent) => {
-                return this.modifyLinks(fileContent, file.path)
+                return this.modifyLinks(fileContent, file.path, metadata)
             })
         }
     }
@@ -196,6 +169,9 @@ export default class AutomaticLinkerPlugin extends Plugin {
     async buildUrlTitleMap() {
         const activeFile = this.app.workspace.getActiveFile()
         if (!activeFile) return
+        const metadata = this.app.metadataCache.getFileCache(activeFile)?.frontmatter
+        if (isUrlTitleReplacementOff(metadata)) return
+
         const fileContent = await this.app.vault.read(activeFile)
         const { contentStart } = getFrontMatterInfo(fileContent)
         const body = fileContent.slice(contentStart)
@@ -204,15 +180,32 @@ export default class AutomaticLinkerPlugin extends Plugin {
         for (const url of urls) {
             if (this.urlTitleMap.has(url)) continue
 
-            const response = await request(url)
-            const title = getTitleFromHtml(response)
-            this.urlTitleMap.set(url, title)
+            try {
+                const response = await request(url)
+                const title = getTitleFromHtml(response)
+
+                if (title) {
+                    this.urlTitleMap.set(url, title)
+                }
+                else {
+                    if (this.settings.debug) {
+                        console.warn(`Automatic Linker: No title found for URL: ${url}`)
+                    }
+                }
+            }
+            catch (error) {
+                if (this.settings.debug) {
+                    console.warn(`Automatic Linker: Failed to fetch URL title for: ${url}`, error)
+                }
+            }
         }
     }
 
     async formatThenRunPrettierAndLinter() {
-        await this.buildUrlTitleMap()
-        await this.modifyLinksForActiveFile()
+        if (this.settings.replaceUrlWithTitle) {
+            await this.buildUrlTitleMap()
+        }
+        this.modifyLinksForActiveFile()
 
         if (this.settings.runPrettierAfterFormatting) {
             await sleep(this.settings.formatDelayMs ?? 100)
@@ -239,24 +232,16 @@ export default class AutomaticLinkerPlugin extends Plugin {
         if (!this.trie || !this.candidateMap) return
 
         const linkGenerator = this.createLinkGenerator(activeFile.path)
-        const baseDir = this.settings.respectNewFileFolderPath
-            ? this.app.vault.getConfig("newFileFolderPath")
-            : undefined
-        const updatedText = replaceLinks({
+        const baseDir = this.settings.respectNewFileFolderPath ? this.app.vault.getConfig("newFileFolderPath") : undefined
+        const updatedText = formatMarkdownSelection({
             body: selectedText,
-            linkResolverContext: {
-                filePath: activeFile.path.replace(/\.md$/, ""),
+            filePath: activeFile.path,
+            settings: this.settings,
+            baseDir,
+            candidateIndex: {
                 trie: this.trie,
                 candidateMap: this.candidateMap,
             },
-            settings: {
-                proximityBasedLinking: this.settings.proximityBasedLinking,
-                baseDir,
-                ignoreDateFormats: this.settings.ignoreDateFormats,
-                ignoreCase: this.settings.ignoreCase,
-                preventSelfLinking: this.settings.preventSelfLinking,
-                removeAliasInDirs: this.settings.removeAliasInDirs,
-            },
             linkGenerator,
         })
         cm.replaceSelection(updatedText)
@@ -268,14 +253,9 @@ export default class AutomaticLinkerPlugin extends Plugin {
             .filter((file) => {
                 // Filter out files in excluded directories
                 const path = file.path.replace(/\.md$/, "")
-                return !this.settings.excludeDirsFromAutoLinking.some(
-                    (excludeDir) => {
-                        return (
-                            path.startsWith(excludeDir + "/")
-                            || path === excludeDir
-                        )
-                    },
-                )
+                return !this.settings.excludeDirsFromAutoLinking.some((excludeDir) => {
+                    return (path.startsWith(excludeDir + "/") || path === excludeDir)
+                })
             })
             .map((file) => {
                 // Remove the .md extension
@@ -286,11 +266,8 @@ export default class AutomaticLinkerPlugin extends Plugin {
                 const exclude = isLinkingExcluded(metadata)
 
                 const aliases = (() => {
-                    if (this.settings.considerAliases) {
-                        const frontmatter
-                            = this.app.metadataCache.getFileCache(
-                                file,
-                            )?.frontmatter
+                    if (this.settings.includeAliases) {
+                        const frontmatter = this.app.metadataCache.getFileCache(file)?.frontmatter
                         const aliases = parseFrontMatterAliases(frontmatter)
                         return aliases
                     }
@@ -318,9 +295,6 @@ export default class AutomaticLinkerPlugin extends Plugin {
         this.candidateMap = candidateMap
         this.trie = trie
 
-        // Clear frontmatter cache when Trie is rebuilt
-        this.frontmatterCache.clear()
-
         if (this.settings.showNotice) {
             new Notice(`Automatic Linker: Loaded all markdown files. (${allFiles.length} files)`)
         }
@@ -330,8 +304,7 @@ export default class AutomaticLinkerPlugin extends Plugin {
     }
 
     private refreshFileDataAndTrieOnFrontmatterChange(file: TFile) {
-        const metadata
-            = this.app.metadataCache.getFileCache(file)?.frontmatter
+        const metadata = this.app.metadataCache.getFileCache(file)?.frontmatter
 
         // Extract frontmatter fields that affect the Trie
         const relevantFields = {
@@ -355,8 +328,14 @@ export default class AutomaticLinkerPlugin extends Plugin {
         }
     }
 
-    async onload() {
-        await this.loadSettings()
+    onload() {
+        runAsyncSafely(async () => {
+            await this.loadSettings()
+            this.initializePlugin()
+        })
+    }
+
+    private initializePlugin() {
         this.addSettingTab(new AutomaticLinkerPluginSettingsTab(this.app, this))
 
         // Load file data and build the Trie when the layout is ready.
@@ -364,14 +343,10 @@ export default class AutomaticLinkerPlugin extends Plugin {
             this.refreshFileDataAndTrie()
 
             this.registerEvent(
-                this.app.vault.on("delete", () =>
-                    this.refreshFileDataAndTrie(),
-                ),
+                this.app.vault.on("delete", () => this.refreshFileDataAndTrie()),
             )
             this.registerEvent(
-                this.app.vault.on("create", () =>
-                    this.refreshFileDataAndTrie(),
-                ),
+                this.app.vault.on("create", () => this.refreshFileDataAndTrie()),
             )
             this.registerEvent(
                 this.app.vault.on("rename", () =>
@@ -379,9 +354,7 @@ export default class AutomaticLinkerPlugin extends Plugin {
                 ),
             )
             this.registerEvent(
-                this.app.metadataCache.on("changed", file =>
-                    this.refreshFileDataAndTrieOnFrontmatterChange(file),
-                ),
+                this.app.metadataCache.on("changed", file => this.refreshFileDataAndTrieOnFrontmatterChange(file)),
             )
         })
 
@@ -446,14 +419,12 @@ export default class AutomaticLinkerPlugin extends Plugin {
             name: "Copy file without links",
             editorCallback: async () => {
                 const activeFile = this.app.workspace.getActiveFile()
-                if (!activeFile) {
-                    return
-                }
+                if (!activeFile) return
                 const fileContent = await this.app.vault.read(activeFile)
                 const { contentStart } = getFrontMatterInfo(fileContent)
                 const body = fileContent.slice(contentStart)
                 const bodyWithoutLinks = excludeLinks(body)
-                navigator.clipboard.writeText(bodyWithoutLinks)
+                await navigator.clipboard.writeText(bodyWithoutLinks)
             },
         })
 
@@ -471,9 +442,7 @@ export default class AutomaticLinkerPlugin extends Plugin {
                     { line: to.line, ch: editor.getLine(to.line).length },
                 )
 
-                if (!selectedText) {
-                    return
-                }
+                if (!selectedText) return
 
                 // Remove minimal indent
                 const textWithMinimalIndent = removeMinimalIndent(selectedText)
@@ -484,46 +453,117 @@ export default class AutomaticLinkerPlugin extends Plugin {
             },
         })
 
+        this.addCommand({
+            id: "ai-link-enhancer",
+            name: "Run AI Link Enhancer",
+            icon: "sparkles",
+            editorCallback: async (editor: Editor) => {
+                if (!this.settings.aiEnabled) {
+                    new Notice("AI Link Enhancement is not enabled in settings.")
+                    return
+                }
+
+                const activeFile = this.app.workspace.getActiveFile()
+                if (!activeFile) return
+
+                const noticeFragment = activeDocument.createDocumentFragment()
+                const container = noticeFragment.createEl("div")
+                container.createEl("div", { text: "AI Link Enhancer: Analyzing context..." })
+                const progress = container.createEl("progress")
+                progress.setAttr("style", "width: 100%; height: 10px;")
+                const notice = new Notice(noticeFragment, 0)
+
+                try {
+                    const fileContent = await this.app.vault.read(activeFile)
+                    const { contentStart } = getFrontMatterInfo(fileContent)
+                    const body = fileContent.slice(contentStart)
+                    const normalizedActiveFilePath = activeFile.path.replace(/\.md$/, "")
+                    const baseDir = this.settings.respectNewFileFolderPath
+                        ? this.app.vault.getConfig("newFileFolderPath")
+                        : undefined
+
+                    if (!this.candidateMap || !this.trie) {
+                        this.refreshFileDataAndTrie()
+                    }
+
+                    if (!this.candidateMap || !this.trie) {
+                        new Notice("Failed to build index.")
+                        return
+                    }
+
+                    const resolvedAmbiguitiesResult = await resolveAmbiguities(
+                        body,
+                        this.candidateMap,
+                        this.trie,
+                        this.settings,
+                        normalizedActiveFilePath,
+                        baseDir,
+                    )
+
+                    const resultBody = replaceLinks({
+                        body,
+                        linkResolverContext: {
+                            filePath: normalizedActiveFilePath,
+                            trie: this.trie,
+                            candidateMap: this.candidateMap,
+                        },
+                        settings: toReplaceLinksSettings(
+                            this.settings,
+                            baseDir,
+                        ),
+                        resolvedAmbiguities: resolvedAmbiguitiesResult,
+                    })
+
+                    if (body !== resultBody) {
+                        updateEditor(body, resultBody, editor)
+                        new Notice("AI Link Enhancement completed.")
+                    }
+                    else {
+                        new Notice("No links to enhance.")
+                    }
+                }
+                catch (error) {
+                    console.error("AI Link Enhancer error:", error)
+                    new Notice("AI Link Enhancement failed. Check console for details.")
+                }
+                finally {
+                    notice.hide()
+                }
+            },
+        })
+
         // Optionally, override the default save command to run modifyLinks (throttled).
-        const saveCommandDefinition
-        // @ts-ignore
-            = this.app?.commands?.commands?.["editor:save-file"]
+        const saveCommandDefinition = this.app?.commands?.commands?.["editor:save-file"]
         const saveCallback = saveCommandDefinition?.checkCallback
         if (typeof saveCallback === "function") {
             // Preserve the original save callback to call it after modifying links.
             this.originalSaveCallback = saveCallback
         }
 
-        saveCommandDefinition.checkCallback = async (checking: boolean) => {
+        saveCommandDefinition.checkCallback = (checking: boolean) => {
             if (checking) {
                 return saveCallback?.(checking)
             }
             else {
-                if (!this.settings.formatOnSave) {
-                    return
-                }
-                await sleep(this.settings.formatDelayMs ?? 100)
-                await this.formatThenRunPrettierAndLinter()
+                if (!this.settings.formatOnSave) return
+                runAsyncSafely(async () => {
+                    await sleep(this.settings.formatDelayMs ?? 100)
+                    await this.formatThenRunPrettierAndLinter()
+                })
             }
         }
     }
 
-    async onunload() {
+    onunload() {
         // Restore original save command callback
-        const saveCommandDefinition
-        // @ts-ignore
-            = this.app?.commands?.commands?.["editor:save-file"]
+        const saveCommandDefinition = this.app?.commands?.commands?.["editor:save-file"]
         if (saveCommandDefinition && this.originalSaveCallback) {
             saveCommandDefinition.checkCallback = this.originalSaveCallback
         }
     }
 
     async loadSettings() {
-        this.settings = Object.assign(
-            {},
-            DEFAULT_SETTINGS,
-            await this.loadData(),
-        )
+        this.settings = Object.assign({}, DEFAULT_SETTINGS, await this.loadData())
     }
 
     async saveSettings() {

src/markdown-protection.ts

@@ -0,0 +1,2 @@
+export const RAW_URL_SOURCE = "(?:https?:\\/\\/|linear:\\/\\/)[^\\s]+"
+export const RAW_URL_AT_START_PATTERN = new RegExp(`^(${RAW_URL_SOURCE})`)

src/markdown-segments.ts

@@ -0,0 +1,309 @@
+import { RAW_URL_SOURCE } from "./markdown-protection"
+
+export type MarkdownSegmentKind = "prose" | "protected"
+
+export type MarkdownProtectedKind = "inline-code"
+    | "fenced-code"
+    | "wikilink"
+    | "markdown-link"
+    | "single-bracket"
+    | "url"
+    | "heading"
+    | "callout"
+    | "table-row"
+
+export interface MarkdownSegment {
+    kind: MarkdownSegmentKind
+    protectedKind?: MarkdownProtectedKind
+    start: number
+    end: number
+    text: string
+}
+
+export interface SegmentMarkdownOptions {
+    protectHeadings?: boolean
+    protectCallouts?: boolean
+    protectTableRows?: boolean
+    protectUrls?: boolean
+}
+
+interface ProtectedRange {
+    start: number
+    end: number
+    protectedKind: MarkdownProtectedKind
+}
+
+export const isMarkdownTableLine = (line: string): boolean => {
+    const trimmedLine = line.trim()
+    if (!trimmedLine || !trimmedLine.includes("|")) {
+        return false
+    }
+
+    if (
+        trimmedLine.startsWith("|")
+        && trimmedLine.endsWith("|")
+        && /^[|:\s-]+$/.test(trimmedLine)
+    ) {
+        return true
+    }
+
+    return trimmedLine.startsWith("|") && trimmedLine.endsWith("|")
+}
+
+const collectHeadingRanges = (text: string): ProtectedRange[] => {
+    const ranges: ProtectedRange[] = []
+    const headingPattern = /^#{1,6}\s+.*$/gm
+    let match: RegExpExecArray | null
+
+    while ((match = headingPattern.exec(text)) !== null) {
+        ranges.push({
+            start: match.index,
+            end: match.index + match[0].length,
+            protectedKind: "heading",
+        })
+    }
+
+    return ranges
+}
+
+const collectCalloutRanges = (text: string): ProtectedRange[] => {
+    const ranges: ProtectedRange[] = []
+    const calloutPattern = /^>[ \t]*\[![\w-]+\].*?(\n>.*?)*(?=\n(?!>)|$)/gm
+    let match: RegExpExecArray | null
+
+    while ((match = calloutPattern.exec(text)) !== null) {
+        ranges.push({
+            start: match.index,
+            end: match.index + match[0].length,
+            protectedKind: "callout",
+        })
+    }
+
+    return ranges
+}
+
+const collectTableRowRanges = (text: string): ProtectedRange[] => {
+    const ranges: ProtectedRange[] = []
+    const linePattern = /[^\n]*(?:\n|$)/g
+    let match: RegExpExecArray | null
+
+    while ((match = linePattern.exec(text)) !== null) {
+        if (match[0] === "") {
+            break
+        }
+
+        const lineText = match[0]
+        const lineContent = lineText.endsWith("\n")
+            ? lineText.slice(0, -1).replace(/\r$/, "")
+            : lineText.replace(/\r$/, "")
+
+        if (isMarkdownTableLine(lineContent)) {
+            ranges.push({
+                start: match.index,
+                end: match.index + lineText.length,
+                protectedKind: "table-row",
+            })
+        }
+    }
+
+    return ranges
+}
+
+const escapeRegExp = (text: string): string =>
+    text.replace(/[.*+?^${}()|[\]\\]/g, "\\$&")
+
+const collectFencedCodeRanges = (text: string): ProtectedRange[] => {
+    if (!text.includes("```") && !text.includes("~~~")) {
+        return []
+    }
+
+    const ranges: ProtectedRange[] = []
+    const openingFencePattern = /^ {0,3}(`{3,}|~{3,})[^\r\n]*(?:\r?\n|$)/gm
+    let openingMatch: RegExpExecArray | null
+
+    while ((openingMatch = openingFencePattern.exec(text)) !== null) {
+        const openingFence = openingMatch[1]
+        const fenceChar = openingFence[0]
+        const fenceLength = openingFence.length
+        const closingFencePattern = new RegExp(
+            `^ {0,3}${escapeRegExp(fenceChar)}{${fenceLength},}[ \\t]*(?:\\r?\\n|$)`,
+            "gm",
+        )
+        closingFencePattern.lastIndex = openingMatch.index + openingMatch[0].length
+        const closingMatch = closingFencePattern.exec(text)
+        const end = closingMatch
+            ? closingMatch.index + closingMatch[0].length
+            : text.length
+
+        ranges.push({
+            start: openingMatch.index,
+            end,
+            protectedKind: "fenced-code",
+        })
+        openingFencePattern.lastIndex = end
+    }
+
+    return ranges
+}
+
+const buildProtectedPattern = (protectUrls: boolean): RegExp => {
+    const parts = [
+        "`[^`]*`",
+        "\\[\\[[^\\]]+\\]\\]",
+        "\\[[^\\]]+\\]\\([^)]+\\)",
+        "\\[[^\\]]+\\]",
+    ]
+
+    if (protectUrls) {
+        parts.push(RAW_URL_SOURCE)
+    }
+
+    return new RegExp(`(${parts.join("|")})`, "g")
+}
+
+const getProtectedKind = (text: string): MarkdownProtectedKind => {
+    if (text.startsWith("```") || text.startsWith("~~~")) {
+        return "fenced-code"
+    }
+
+    if (text.startsWith("`")) {
+        return "inline-code"
+    }
+
+    if (text.startsWith("[[")) {
+        return "wikilink"
+    }
+
+    if (text.startsWith("[")) {
+        return text.includes("](") ? "markdown-link" : "single-bracket"
+    }
+
+    return "url"
+}
+
+const sortAndMergeRanges = (ranges: ProtectedRange[]): ProtectedRange[] => {
+    const sortedRanges = ranges
+        .slice()
+        .sort((a, b) => a.start - b.start || a.end - b.end)
+    const merged: ProtectedRange[] = []
+
+    for (const range of sortedRanges) {
+        const lastRange = merged[merged.length - 1]
+        if (!lastRange || range.start >= lastRange.end) {
+            merged.push({ ...range })
+            continue
+        }
+
+        lastRange.end = Math.max(lastRange.end, range.end)
+    }
+
+    return merged
+}
+
+const isInsideRanges = (
+    index: number,
+    ranges: ProtectedRange[],
+): boolean => {
+    return ranges.some(range => index >= range.start && index < range.end)
+}
+
+export const segmentMarkdown = (
+    text: string,
+    options: SegmentMarkdownOptions = {},
+): MarkdownSegment[] => {
+    const mayContainProtectedMarkdown = text.includes("`")
+        || text.includes("~")
+        || text.includes("[")
+        || (options.protectHeadings && text.includes("#"))
+        || (options.protectCallouts && text.includes(">"))
+        || (options.protectTableRows && text.includes("|"))
+        || (options.protectUrls
+            && (text.includes("http") || text.includes("linear://")))
+
+    if (!mayContainProtectedMarkdown) {
+        return [{
+            kind: "prose",
+            start: 0,
+            end: text.length,
+            text,
+        }]
+    }
+
+    const ranges: ProtectedRange[] = []
+
+    if (options.protectHeadings) {
+        ranges.push(...collectHeadingRanges(text))
+    }
+
+    if (options.protectCallouts) {
+        ranges.push(...collectCalloutRanges(text))
+    }
+
+    if (options.protectTableRows) {
+        ranges.push(...collectTableRowRanges(text))
+    }
+
+    ranges.push(...collectFencedCodeRanges(text))
+
+    const protectedPattern = buildProtectedPattern(options.protectUrls ?? false)
+    let match: RegExpExecArray | null
+
+    while ((match = protectedPattern.exec(text)) !== null) {
+        if (isInsideRanges(match.index, ranges)) {
+            continue
+        }
+
+        ranges.push({
+            start: match.index,
+            end: match.index + match[0].length,
+            protectedKind: getProtectedKind(match[0]),
+        })
+    }
+
+    const mergedRanges = sortAndMergeRanges(ranges)
+    const segments: MarkdownSegment[] = []
+    let cursor = 0
+
+    for (const range of mergedRanges) {
+        if (cursor < range.start) {
+            segments.push({
+                kind: "prose",
+                start: cursor,
+                end: range.start,
+                text: text.slice(cursor, range.start),
+            })
+        }
+
+        segments.push({
+            kind: "protected",
+            protectedKind: range.protectedKind,
+            start: range.start,
+            end: range.end,
+            text: text.slice(range.start, range.end),
+        })
+        cursor = range.end
+    }
+
+    if (cursor < text.length || segments.length === 0) {
+        segments.push({
+            kind: "prose",
+            start: cursor,
+            end: text.length,
+            text: text.slice(cursor),
+        })
+    }
+
+    return segments
+}
+
+export const mapMarkdownProse = (
+    text: string,
+    transform: (segmentText: string, segment: MarkdownSegment) => string,
+    options: SegmentMarkdownOptions = {},
+): string => {
+    return segmentMarkdown(text, options)
+        .map(segment => segment.kind === "prose"
+            ? transform(segment.text, segment)
+            : segment.text)
+        .join("")
+}

src/plugin-compat.ts

@@ -0,0 +1,15 @@
+export function sleep(
+    ms: number,
+    scheduleTimeout: (callback: () => void, delay: number) => unknown = window.setTimeout.bind(window),
+): Promise<void> {
+    return new Promise((resolve) => {
+        scheduleTimeout(resolve, ms)
+    })
+}
+
+export function runAsyncSafely(
+    task: () => Promise<void>,
+    onError: (error: unknown) => void = console.error,
+): void {
+    void task().catch(onError)
+}

src/replace-links/__tests__/ai-disambiguation.test.ts

@@ -0,0 +1,117 @@
+import { describe, it, expect } from "vitest"
+import { replaceLinks } from "../replace-links"
+import { buildCandidateTrie } from "../../trie"
+import { resolveAmbiguities } from "../../utils/resolve-ambiguities"
+import { DEFAULT_SETTINGS } from "../../settings/settings-info"
+
+describe("replaceLinks with AI disambiguation", () => {
+    const allFiles = [
+        { path: "work/meeting", scoped: false, aliases: [] },
+        { path: "private/meeting", scoped: false, aliases: [] },
+    ]
+    const { candidateMap, trie } = buildCandidateTrie(allFiles, undefined, true)
+    const context = {
+        filePath: "test.md",
+        trie,
+        candidateMap,
+    }
+
+    it("should use the AI-resolved path for unlinked words", () => {
+        const body = "I have a meeting."
+        const resolvedAmbiguities = new Map([["meeting", "work/meeting"]])
+
+        const result = replaceLinks({
+            body,
+            linkResolverContext: context,
+            resolvedAmbiguities,
+        })
+
+        expect(result).toBe("I have a [[work/meeting|meeting]].")
+    })
+
+    it("should correct existing links if resolvedAmbiguities contains them", () => {
+        const body = "Check [[private/meeting|meeting]] notes."
+        const resolvedAmbiguities = new Map([["[[private/meeting|meeting]]", "work/meeting"]])
+
+        const result = replaceLinks({
+            body,
+            linkResolverContext: context,
+            resolvedAmbiguities,
+        })
+
+        expect(result).toBe("Check [[work/meeting|meeting]] notes.")
+    })
+
+    it("should handle existing links without alias for correction", () => {
+        const body = "Check [[private/meeting]] notes."
+        // The resolveAmbiguities scanner uses the full link as key
+        const resolvedAmbiguities = new Map([["[[private/meeting]]", "work/meeting"]])
+
+        const result = replaceLinks({
+            body,
+            linkResolverContext: context,
+            resolvedAmbiguities,
+        })
+
+        expect(result).toBe("Check [[work/meeting|private/meeting]] notes.")
+    })
+
+    it("should honor AI-resolved Korean suffix choices", () => {
+        const koreanFiles = [
+            { path: "work/문서", scoped: false, aliases: [] },
+            { path: "private/문서", scoped: false, aliases: [] },
+        ]
+        const { candidateMap: koreanCandidateMap, trie: koreanTrie } = buildCandidateTrie(
+            koreanFiles,
+            undefined,
+            true,
+        )
+        const body = "문서이다."
+        const resolvedAmbiguities = new Map([["문서", "private/문서"]])
+
+        const result = replaceLinks({
+            body,
+            linkResolverContext: {
+                filePath: "test.md",
+                trie: koreanTrie,
+                candidateMap: koreanCandidateMap,
+            },
+            resolvedAmbiguities,
+        })
+
+        expect(result).toBe("[[private/문서|문서]]이다.")
+    })
+
+    it("should keep AI command self-link prevention when the active file path includes .md", async () => {
+        const body = "meeting"
+        const activeFilePath = "work/meeting.md"
+        const normalizedFilePath = activeFilePath.replace(/\.md$/, "")
+        const settings = {
+            ...DEFAULT_SETTINGS,
+            aiEnabled: true,
+            preventSelfLinking: true,
+        }
+
+        const resolvedAmbiguities = await resolveAmbiguities(
+            body,
+            candidateMap,
+            trie,
+            settings,
+            normalizedFilePath,
+        )
+
+        const result = replaceLinks({
+            body,
+            linkResolverContext: {
+                filePath: normalizedFilePath,
+                trie,
+                candidateMap,
+            },
+            settings,
+            resolvedAmbiguities,
+        })
+
+        expect(resolvedAmbiguities.size).toBe(0)
+        expect(result).toBe("meeting")
+    })
+})

src/replace-links/__tests__/candidate-scanner.test.ts

@@ -0,0 +1,506 @@
+import { describe, expect, it } from "vitest"
+import { buildTrie, CandidateData } from "../../trie"
+import { buildCandidateTrieForTest } from "./test-helpers"
+import { replaceLinks } from "../replace-links"
+import {
+    getOccurrenceContext,
+    scanCandidateOccurrences,
+} from "../candidate-scanner"
+
+describe("scanCandidateOccurrences", () => {
+    it("reports ambiguous prose candidates and skips inline code", () => {
+        const { candidateMap, trie } = buildCandidateTrieForTest({
+            files: [
+                { path: "work/meeting" },
+                { path: "private/meeting" },
+            ],
+            settings: {
+                scoped: false,
+                baseDir: undefined,
+                ignoreCase: true,
+            },
+        })
+
+        const occurrences = scanCandidateOccurrences({
+            text: "`meeting` meeting",
+            filePath: "notes/today",
+            trie,
+            candidateMap,
+            settings: { ignoreCase: true, proximityBasedLinking: true },
+        })
+
+        expect(occurrences.map(o => ({
+            kind: o.kind,
+            text: o.text,
+            start: o.start,
+            end: o.end,
+            candidates: o.candidateData.candidates.map(c => c.canonical),
+        }))).toEqual([
+            {
+                kind: "unlinked",
+                text: "meeting",
+                start: 10,
+                end: 17,
+                candidates: ["work/meeting", "private/meeting"],
+            },
+        ])
+    })
+
+    it("reports existing wikilinks by their display alias", () => {
+        const { candidateMap, trie } = buildCandidateTrieForTest({
+            files: [
+                { path: "work/meeting" },
+                { path: "private/meeting" },
+            ],
+            settings: {
+                scoped: false,
+                baseDir: undefined,
+                ignoreCase: true,
+            },
+        })
+
+        const occurrences = scanCandidateOccurrences({
+            text: "Check [[private/meeting|meeting]] notes.",
+            filePath: "notes/today",
+            trie,
+            candidateMap,
+            settings: { ignoreCase: true, proximityBasedLinking: true },
+        })
+
+        expect(occurrences.map(o => ({
+            kind: o.kind,
+            text: o.text,
+            candidateKey: o.candidateKey,
+            candidates: o.candidateData.candidates.map(c => c.canonical),
+        }))).toEqual([
+            {
+                kind: "existing-wikilink",
+                text: "[[private/meeting|meeting]]",
+                candidateKey: "meeting",
+                candidates: ["work/meeting", "private/meeting"],
+            },
+        ])
+    })
+
+    it("skips existing wikilinks inside inline code", () => {
+        const { candidateMap, trie } = buildCandidateTrieForTest({
+            files: [
+                { path: "work/meeting" },
+                { path: "private/meeting" },
+            ],
+            settings: {
+                scoped: false,
+                baseDir: undefined,
+                ignoreCase: true,
+            },
+        })
+
+        const occurrences = scanCandidateOccurrences({
+            text: "`[[private/meeting|meeting]]`",
+            filePath: "notes/today",
+            trie,
+            candidateMap,
+            settings: { ignoreCase: true, proximityBasedLinking: true },
+        })
+
+        expect(occurrences).toEqual([])
+    })
+
+    it("preserves trie-hit candidate sets for scoped candidates in the current namespace", () => {
+        const { candidateMap, trie } = buildCandidateTrieForTest({
+            files: [
+                { path: "pages/team-a/internal" },
+                { path: "pages/team-b/internal" },
+            ],
+            settings: {
+                scoped: true,
+                baseDir: "pages",
+                ignoreCase: true,
+            },
+        })
+
+        const occurrences = scanCandidateOccurrences({
+            text: "internal",
+            filePath: "pages/team-a/today",
+            trie,
+            candidateMap,
+            settings: {
+                baseDir: "pages",
+                ignoreCase: true,
+                proximityBasedLinking: true,
+            },
+        })
+
+        expect(occurrences).toHaveLength(1)
+        expect(occurrences[0].candidateData.candidates.map(c => c.canonical)).toEqual([
+            "pages/team-a/internal",
+            "pages/team-b/internal",
+        ])
+    })
+
+    it("matches replaceLinks trie-hit namespace semantics", () => {
+        const candidateMap = new Map<string, CandidateData>([
+            [
+                "internal",
+                {
+                    candidates: [
+                        {
+                            canonical: "pages/team-b/internal",
+                            scoped: true,
+                            namespace: "team-b",
+                        },
+                        {
+                            canonical: "pages/team-a/internal",
+                            scoped: true,
+                            namespace: "team-a",
+                        },
+                    ],
+                },
+            ],
+        ])
+        const trie = buildTrie(["internal"], true)
+
+        const occurrences = scanCandidateOccurrences({
+            text: "internal",
+            filePath: "pages/team-a/today",
+            trie,
+            candidateMap,
+            settings: {
+                baseDir: "pages",
+                ignoreCase: true,
+                proximityBasedLinking: true,
+            },
+        })
+
+        expect(occurrences).toEqual([])
+    })
+
+    it("matches replaceLinks scoped namespace behavior when baseDir is set", () => {
+        const settings = {
+            scoped: true,
+            baseDir: "pages",
+            ignoreCase: true,
+            proximityBasedLinking: true,
+        }
+        const { candidateMap, trie } = buildCandidateTrieForTest({
+            files: [
+                { path: "pages/team-a/internal" },
+                { path: "pages/team-a/archive/internal" },
+            ],
+            settings,
+        })
+
+        const occurrences = scanCandidateOccurrences({
+            text: "internal",
+            filePath: "pages/team-a/today",
+            trie,
+            candidateMap,
+            settings,
+        })
+        const replaced = replaceLinks({
+            body: "internal",
+            linkResolverContext: {
+                filePath: "pages/team-a/today",
+                trie,
+                candidateMap,
+            },
+            settings,
+        })
+
+        expect(occurrences.map(o => ({
+            text: o.text,
+            candidates: o.candidateData.candidates.map(c => c.canonical),
+        }))).toEqual([
+            {
+                text: "internal",
+                candidates: [
+                    "pages/team-a/internal",
+                    "pages/team-a/archive/internal",
+                ],
+            },
+        ])
+        expect(replaced).toBe("[[team-a/archive/internal|internal]]")
+    })
+
+    it("matches replaceLinks by protecting raw Linear URLs", () => {
+        const settings = {
+            scoped: false,
+            baseDir: undefined,
+            ignoreCase: true,
+            proximityBasedLinking: true,
+        }
+        const { candidateMap, trie } = buildCandidateTrieForTest({
+            files: [
+                { path: "work/linear" },
+                { path: "private/linear" },
+            ],
+            settings,
+        })
+        const body = "Open linear://issue/TEAM-123 then linear"
+        const expectedStart = body.lastIndexOf("linear")
+
+        const occurrences = scanCandidateOccurrences({
+            text: body,
+            filePath: "notes/today",
+            trie,
+            candidateMap,
+            settings,
+        })
+        const replaced = replaceLinks({
+            body,
+            linkResolverContext: {
+                filePath: "notes/today",
+                trie,
+                candidateMap,
+            },
+            settings,
+        })
+
+        expect(occurrences.map(o => ({
+            text: o.text,
+            start: o.start,
+            end: o.end,
+        }))).toEqual([
+            {
+                text: "linear",
+                start: expectedStart,
+                end: expectedStart + "linear".length,
+            },
+        ])
+        expect(replaced).toBe(
+            "Open linear://issue/TEAM-123 then [[private/linear|linear]]",
+        )
+    })
+
+    it("skips fenced code blocks, callouts, and ignored headings", () => {
+        const { candidateMap, trie } = buildCandidateTrieForTest({
+            files: [{ path: "meeting" }],
+            settings: {
+                scoped: false,
+                baseDir: undefined,
+                ignoreCase: true,
+            },
+        })
+
+        const occurrences = scanCandidateOccurrences({
+            text: `# meeting
+> [!note]
+> meeting
+
+~~~ts
+meeting
+~~~
+
+meeting`,
+            filePath: "notes/today",
+            trie,
+            candidateMap,
+            settings: {
+                ignoreCase: true,
+                ignoreHeadings: true,
+                proximityBasedLinking: true,
+            },
+        })
+
+        expect(occurrences.map(o => ({
+            start: o.start,
+            end: o.end,
+            text: o.text,
+        }))).toEqual([
+            {
+                start: 50,
+                end: 57,
+                text: "meeting",
+            },
+        ])
+    })
+
+    it("does not re-enter a later callout when inline code appears earlier", () => {
+        const { candidateMap, trie } = buildCandidateTrieForTest({
+            files: [
+                { path: "work/meeting" },
+                { path: "private/meeting" },
+            ],
+            settings: {
+                scoped: false,
+                baseDir: undefined,
+                ignoreCase: true,
+            },
+        })
+
+        const occurrences = scanCandidateOccurrences({
+            text: "`meeting`\n\n> [!note]\n> meeting\n\nmeeting",
+            filePath: "notes/today",
+            trie,
+            candidateMap,
+            settings: {
+                ignoreCase: true,
+                proximityBasedLinking: true,
+            },
+        })
+
+        expect(occurrences.map(o => ({
+            start: o.start,
+            end: o.end,
+            text: o.text,
+        }))).toEqual([
+            {
+                start: 32,
+                end: 39,
+                text: "meeting",
+            },
+        ])
+    })
+
+    it("skips ignored Markdown table rows but still finds prose outside the table", () => {
+        const { candidateMap, trie } = buildCandidateTrieForTest({
+            files: [
+                { path: "work/meeting" },
+                { path: "private/meeting" },
+            ],
+            settings: {
+                scoped: false,
+                baseDir: undefined,
+                ignoreCase: true,
+            },
+        })
+
+        const text = `| Topic |
+| --- |
+| meeting |
+
+meeting`
+
+        const occurrences = scanCandidateOccurrences({
+            text,
+            filePath: "notes/today",
+            trie,
+            candidateMap,
+            settings: {
+                ignoreCase: true,
+                ignoreMarkdownTables: true,
+                proximityBasedLinking: true,
+            },
+        })
+
+        expect(occurrences.map(o => ({
+            kind: o.kind,
+            text: o.text,
+            start: o.start,
+            end: o.end,
+        }))).toEqual([
+            {
+                kind: "unlinked",
+                text: "meeting",
+                start: text.lastIndexOf("meeting"),
+                end: text.lastIndexOf("meeting") + "meeting".length,
+            },
+        ])
+    })
+
+    it("skips existing wikilinks inside ignored Markdown table rows", () => {
+        const { candidateMap, trie } = buildCandidateTrieForTest({
+            files: [
+                { path: "work/meeting" },
+                { path: "private/meeting" },
+            ],
+            settings: {
+                scoped: false,
+                baseDir: undefined,
+                ignoreCase: true,
+            },
+        })
+
+        const occurrences = scanCandidateOccurrences({
+            text: `| Topic |
+| --- |
+| [[private/meeting|meeting]] |`,
+            filePath: "notes/today",
+            trie,
+            candidateMap,
+            settings: {
+                ignoreCase: true,
+                ignoreMarkdownTables: true,
+                proximityBasedLinking: true,
+            },
+        })
+
+        expect(occurrences).toEqual([])
+    })
+
+    it("skips Korean particle hits but still finds overlapping follow-on candidates", () => {
+        const isolatedFixture = buildCandidateTrieForTest({
+            files: [
+                { path: "work/문서" },
+                { path: "private/문서" },
+            ],
+            settings: {
+                scoped: false,
+                baseDir: undefined,
+                ignoreCase: true,
+            },
+        })
+        const isolatedOccurrences = scanCandidateOccurrences({
+            text: "문서는",
+            filePath: "notes/today",
+            trie: isolatedFixture.trie,
+            candidateMap: isolatedFixture.candidateMap,
+            settings: { ignoreCase: true, proximityBasedLinking: true },
+        })
+
+        expect(isolatedOccurrences).toEqual([])
+
+        const overlappingFixture = buildCandidateTrieForTest({
+            files: [
+                { path: "work/문서" },
+                { path: "private/문서" },
+                { path: "work/서는" },
+                { path: "private/서는" },
+            ],
+            settings: {
+                scoped: false,
+                baseDir: undefined,
+                ignoreCase: true,
+            },
+        })
+        const { candidateMap, trie } = overlappingFixture
+
+        const overlappingOccurrences = scanCandidateOccurrences({
+            text: "문서는",
+            filePath: "notes/today",
+            trie,
+            candidateMap,
+            settings: { ignoreCase: true, proximityBasedLinking: true },
+        })
+
+        expect(overlappingOccurrences.map(o => ({
+            text: o.text,
+            start: o.start,
+            end: o.end,
+        }))).toEqual([
+            {
+                text: "서는",
+                start: 1,
+                end: 3,
+            },
+        ])
+    })
+})
+
+describe("getOccurrenceContext", () => {
+    it("returns bounded surrounding text for AI requests", () => {
+        const occurrence = {
+            kind: "unlinked" as const,
+            start: 10,
+            end: 17,
+            text: "meeting",
+            candidateKey: "meeting",
+            candidateData: { candidates: [] },
+            isInTable: false,
+        }
+
+        expect(getOccurrenceContext("before -- meeting -- after", occurrence, 4)).toBe(
+            " -- meeting -- ",
+        )
+    })
+})

src/replace-links/__tests__/prev.test.ts

@@ -1046,34 +1046,42 @@ describe("replaceLinks (manual candidateMap/trie)", () => {
         [
             "x",
             {
-                canonical: "namespace/x",
-                scoped: true,
-                namespace: "namespace",
+                candidates: [{
+                    canonical: "namespace/x",
+                    scoped: true,
+                    namespace: "namespace",
+                }],
             },
         ],
         [
             "z",
             {
-                canonical: "namespace/y/z",
-                scoped: true,
-                namespace: "namespace",
+                candidates: [{
+                    canonical: "namespace/y/z",
+                    scoped: true,
+                    namespace: "namespace",
+                }],
             },
         ],
         [
             "root",
             {
-                canonical: "root-note",
-                scoped: true,
-                namespace: "",
+                candidates: [{
+                    canonical: "root-note",
+                    scoped: true,
+                    namespace: "",
+                }],
             },
         ],
         // Candidate without namespace restriction.
         [
             "free",
             {
-                canonical: "free-note",
-                scoped: false,
-                namespace: "other",
+                candidates: [{
+                    canonical: "free-note",
+                    scoped: false,
+                    namespace: "other",
+                }],
             },
         ],
         // For alias testing:
@@ -1081,71 +1089,87 @@ describe("replaceLinks (manual candidateMap/trie)", () => {
         [
             "pages/HelloWorld",
             {
-                canonical: "pages/HelloWorld",
-                scoped: false,
-                namespace: "pages",
+                candidates: [{
+                    canonical: "pages/HelloWorld",
+                    scoped: false,
+                    namespace: "pages",
+                }],
             },
         ],
         // Alias "Hello" is different from the shorthand, so canonical becomes "pages/HelloWorld|Hello".
         [
             "Hello",
             {
-                canonical: "pages/HelloWorld|Hello",
-                scoped: false,
-                namespace: "pages",
+                candidates: [{
+                    canonical: "pages/HelloWorld|Hello",
+                    scoped: false,
+                    namespace: "pages",
+                }],
             },
         ],
         // Also register the shorthand candidate.
         [
             "HelloWorld",
             {
-                canonical: "HelloWorld",
-                scoped: false,
-                namespace: "pages",
+                candidates: [{
+                    canonical: "HelloWorld",
+                    scoped: false,
+                    namespace: "pages",
+                }],
             },
         ],
         // For "tags" test: candidate key "tags" should map to canonical "tags"
         [
             "pages/tags",
             {
-                canonical: "pages/tags",
-                scoped: false,
-                namespace: "pages",
+                candidates: [{
+                    canonical: "pages/tags",
+                    scoped: false,
+                    namespace: "pages",
+                }],
             },
         ],
         [
             "tags",
             {
-                canonical: "tags",
-                scoped: false,
-                namespace: "pages",
+                candidates: [{
+                    canonical: "tags",
+                    scoped: false,
+                    namespace: "pages",
+                }],
             },
         ],
         // For Korean test, add candidate "문서"
         [
             "문서",
             {
-                canonical: "문서",
-                scoped: false,
-                namespace: "namespace",
+                candidates: [{
+                    canonical: "문서",
+                    scoped: false,
+                    namespace: "namespace",
+                }],
             },
         ],
         // For Japanese test, add candidate "ひらがな"
         [
             "ひらがな",
             {
-                canonical: "ひらがな",
-                scoped: false,
-                namespace: "namespace",
+                candidates: [{
+                    canonical: "ひらがな",
+                    scoped: false,
+                    namespace: "namespace",
+                }],
             },
         ],
         // For Chinese test, add candidate "文档"
         [
             "文档",
             {
-                canonical: "文档",
-                scoped: false,
-                namespace: "namespace",
+                candidates: [{
+                    canonical: "文档",
+                    scoped: false,
+                    namespace: "namespace",
+                }],
             },
         ],
     ])
@@ -1266,9 +1290,11 @@ describe("replaceLinks (manual candidateMap/trie)", () => {
         // Add candidate "a" corresponding to a file at "pages/set/a"
         // with scoped enabled and an effective namespace of "set".
         candidateMap.set("a", {
-            canonical: "set/a",
-            scoped: true,
-            namespace: "set",
+            candidates: [{
+                canonical: "set/a",
+                scoped: true,
+                namespace: "set",
+            }],
         })
         const trie = buildTrie(Array.from(candidateMap.keys()))
 

src/replace-links/__tests__/replace-links.code.test.ts

@@ -44,4 +44,89 @@ describe("ignore code", () => {
         })
         expect(result).toBe("```typescript\nexample\n```")
     })
+
+    it("tilde code block", () => {
+        const settings = {
+            scoped: false,
+            baseDir: undefined,
+        }
+        const { candidateMap, trie } = buildCandidateTrieForTest({
+            files: [{ path: "example" }, { path: "typescript" }],
+            settings,
+        })
+        const result = replaceLinks({
+            body: "~~~typescript\nexample\n~~~",
+            linkResolverContext: {
+                filePath: "journals/2022-01-01",
+                trie,
+                candidateMap,
+            },
+            settings,
+        })
+        expect(result).toBe("~~~typescript\nexample\n~~~")
+    })
+
+    it("wide code fence with embedded triple backticks", () => {
+        const settings = {
+            scoped: false,
+            baseDir: undefined,
+        }
+        const { candidateMap, trie } = buildCandidateTrieForTest({
+            files: [{ path: "example" }, { path: "typescript" }],
+            settings,
+        })
+        const result = replaceLinks({
+            body: "````\nnot end ```\nexample\n````",
+            linkResolverContext: {
+                filePath: "journals/2022-01-01",
+                trie,
+                candidateMap,
+            },
+            settings,
+        })
+        expect(result).toBe("````\nnot end ```\nexample\n````")
+    })
+
+    it("unclosed code block", () => {
+        const settings = {
+            scoped: false,
+            baseDir: undefined,
+        }
+        const { candidateMap, trie } = buildCandidateTrieForTest({
+            files: [{ path: "example" }, { path: "typescript" }],
+            settings,
+        })
+        const result = replaceLinks({
+            body: "```typescript\nexample",
+            linkResolverContext: {
+                filePath: "journals/2022-01-01",
+                trie,
+                candidateMap,
+            },
+            settings,
+        })
+        expect(result).toBe("```typescript\nexample")
+    })
+
+    it("unclosed code block when headings are ignored", () => {
+        const settings = {
+            scoped: false,
+            baseDir: undefined,
+            ignoreHeadings: true,
+        }
+        const { candidateMap, trie } = buildCandidateTrieForTest({
+            files: [{ path: "example" }, { path: "typescript" }],
+            settings,
+        })
+        const result = replaceLinks({
+            body: "```typescript\nexample",
+            linkResolverContext: {
+                filePath: "journals/2022-01-01",
+                trie,
+                candidateMap,
+            },
+            settings,
+        })
+        expect(result).toBe("```typescript\nexample")
+    })
 })

src/replace-links/__tests__/replace-links.headings.test.ts

@@ -0,0 +1,250 @@
+import { describe, expect, it } from "vitest"
+import { replaceLinks } from "../replace-links"
+import { buildCandidateTrieForTest } from "./test-helpers"
+
+describe("replaceLinks - heading handling", () => {
+    const { candidateMap, trie } = buildCandidateTrieForTest({
+        files: [
+            { path: "VPN" },
+            { path: "SSH" },
+            { path: "Networking" },
+            { path: "Security" },
+        ],
+        settings: {
+            scoped: false,
+            baseDir: undefined,
+        },
+    })
+
+    describe("basic heading protection", () => {
+        it("should not link text inside h1 heading", () => {
+            const input = `# VPN Configuration`
+
+            const result = replaceLinks({
+                body: input,
+                linkResolverContext: {
+                    filePath: "test",
+                    trie,
+                    candidateMap,
+                },
+                settings: { ignoreHeadings: true },
+            })
+
+            expect(result).toBe(input)
+        })
+
+        it("should not link text inside h2 heading", () => {
+            const input = `## SSH Setup`
+
+            const result = replaceLinks({
+                body: input,
+                linkResolverContext: {
+                    filePath: "test",
+                    trie,
+                    candidateMap,
+                },
+                settings: { ignoreHeadings: true },
+            })
+
+            expect(result).toBe(input)
+        })
+
+        it("should not link text inside h3 heading", () => {
+            const input = `### Networking Basics`
+
+            const result = replaceLinks({
+                body: input,
+                linkResolverContext: {
+                    filePath: "test",
+                    trie,
+                    candidateMap,
+                },
+                settings: { ignoreHeadings: true },
+            })
+
+            expect(result).toBe(input)
+        })
+
+        it("should not link text inside h4 heading", () => {
+            const input = `#### Security Overview`
+
+            const result = replaceLinks({
+                body: input,
+                linkResolverContext: {
+                    filePath: "test",
+                    trie,
+                    candidateMap,
+                },
+                settings: { ignoreHeadings: true },
+            })
+
+            expect(result).toBe(input)
+        })
+
+        it("should not link text inside h5 heading", () => {
+            const input = `##### VPN Details`
+
+            const result = replaceLinks({
+                body: input,
+                linkResolverContext: {
+                    filePath: "test",
+                    trie,
+                    candidateMap,
+                },
+                settings: { ignoreHeadings: true },
+            })
+
+            expect(result).toBe(input)
+        })
+
+        it("should not link text inside h6 heading", () => {
+            const input = `###### SSH Notes`
+
+            const result = replaceLinks({
+                body: input,
+                linkResolverContext: {
+                    filePath: "test",
+                    trie,
+                    candidateMap,
+                },
+                settings: { ignoreHeadings: true },
+            })
+
+            expect(result).toBe(input)
+        })
+    })
+
+    describe("text between headings is still linked", () => {
+        it("should link text in body paragraphs between headings", () => {
+            const input = `# Introduction
+
+VPN is important for Security
+
+## Details
+
+SSH is also useful`
+
+            const expected = `# Introduction
+
+[[VPN]] is important for [[Security]]
+
+## Details
+
+[[SSH]] is also useful`
+
+            const result = replaceLinks({
+                body: input,
+                linkResolverContext: {
+                    filePath: "test",
+                    trie,
+                    candidateMap,
+                },
+                settings: { ignoreHeadings: true },
+            })
+
+            expect(result).toBe(expected)
+        })
+    })
+
+    describe("headings with candidate text are not linked", () => {
+        it("should protect heading but link same text in body", () => {
+            const input = `# VPN
+
+VPN is a useful tool`
+
+            const expected = `# VPN
+
+[[VPN]] is a useful tool`
+
+            const result = replaceLinks({
+                body: input,
+                linkResolverContext: {
+                    filePath: "test",
+                    trie,
+                    candidateMap,
+                },
+                settings: { ignoreHeadings: true },
+            })
+
+            expect(result).toBe(expected)
+        })
+    })
+
+    describe("feature disabled", () => {
+        it("should link text in headings when ignoreHeadings is false", () => {
+            const input = `# VPN Configuration`
+
+            const expected = `# [[VPN]] Configuration`
+
+            const result = replaceLinks({
+                body: input,
+                linkResolverContext: {
+                    filePath: "test",
+                    trie,
+                    candidateMap,
+                },
+                settings: { ignoreHeadings: false },
+            })
+
+            expect(result).toBe(expected)
+        })
+    })
+
+    describe("headings with existing wikilinks", () => {
+        it("should preserve existing wikilinks in headings", () => {
+            const input = `# [[VPN]] Configuration`
+
+            const result = replaceLinks({
+                body: input,
+                linkResolverContext: {
+                    filePath: "test",
+                    trie,
+                    candidateMap,
+                },
+                settings: { ignoreHeadings: true },
+            })
+
+            expect(result).toBe(input)
+        })
+    })
+
+    describe("multiple headings in one document", () => {
+        it("should protect all headings in a document", () => {
+            const input = `# VPN Guide
+
+Some text about VPN
+
+## SSH Configuration
+
+More text about SSH
+
+### Networking and Security
+
+Details about Networking and Security`
+
+            const expected = `# VPN Guide
+
+Some text about [[VPN]]
+
+## SSH Configuration
+
+More text about [[SSH]]
+
+### Networking and Security
+
+Details about [[Networking]] and [[Security]]`
+
+            const result = replaceLinks({
+                body: input,
+                linkResolverContext: {
+                    filePath: "test",
+                    trie,
+                    candidateMap,
+                },
+                settings: { ignoreHeadings: true },
+            })
+
+            expect(result).toBe(expected)
+        })
+    })
+})

src/replace-links/__tests__/replace-links.sentence-case.test.ts

@@ -0,0 +1,113 @@
+import { describe, it, expect } from "vitest"
+import { replaceLinks } from "../replace-links"
+import { buildCandidateTrieForTest } from "./test-helpers"
+
+describe("sentence case matching", () => {
+    const buildContext = (ignoreCase: boolean, matchSentenceCase: boolean) => {
+        const settings = {
+            scoped: false,
+            baseDir: undefined,
+            ignoreCase,
+        }
+        const { candidateMap, trie } = buildCandidateTrieForTest({
+            files: [{ path: "my name" }],
+            settings,
+        })
+        return {
+            candidateMap,
+            trie,
+            replaceSettings: {
+                ...settings,
+                matchSentenceCase,
+            },
+        }
+    }
+
+    it("matches sentence-start capitalized text at the beginning of text", () => {
+        const { candidateMap, trie, replaceSettings } = buildContext(false, true)
+        const result = replaceLinks({
+            body: "My name is John",
+            linkResolverContext: { filePath: "test", trie, candidateMap },
+            settings: replaceSettings,
+        })
+        expect(result).toBe("[[my name|My name]] is John")
+    })
+
+    it("does not match mid-sentence capitalized text", () => {
+        const { candidateMap, trie, replaceSettings } = buildContext(false, true)
+        const result = replaceLinks({
+            body: "he knows My name",
+            linkResolverContext: { filePath: "test", trie, candidateMap },
+            settings: replaceSettings,
+        })
+        expect(result).toBe("he knows My name")
+    })
+
+    it("matches lowercase text in mid-sentence (exact match)", () => {
+        const { candidateMap, trie, replaceSettings } = buildContext(false, true)
+        const result = replaceLinks({
+            body: "he knows my name well",
+            linkResolverContext: { filePath: "test", trie, candidateMap },
+            settings: replaceSettings,
+        })
+        expect(result).toBe("he knows [[my name]] well")
+    })
+
+    it("matches after a period and space", () => {
+        const { candidateMap, trie, replaceSettings } = buildContext(false, true)
+        const result = replaceLinks({
+            body: "something happened. My name is John",
+            linkResolverContext: { filePath: "test", trie, candidateMap },
+            settings: replaceSettings,
+        })
+        expect(result).toBe("something happened. [[my name|My name]] is John")
+    })
+
+    it("matches after a newline", () => {
+        const { candidateMap, trie, replaceSettings } = buildContext(false, true)
+        const result = replaceLinks({
+            body: "line one\nMy name is here",
+            linkResolverContext: { filePath: "test", trie, candidateMap },
+            settings: replaceSettings,
+        })
+        expect(result).toBe("line one\n[[my name|My name]] is here")
+    })
+
+    it("does not match when matchSentenceCase is off", () => {
+        const { candidateMap, trie, replaceSettings } = buildContext(false, false)
+        const result = replaceLinks({
+            body: "My name is John",
+            linkResolverContext: { filePath: "test", trie, candidateMap },
+            settings: replaceSettings,
+        })
+        expect(result).toBe("My name is John")
+    })
+
+    it("does not interfere when ignoreCase is on", () => {
+        const { candidateMap, trie, replaceSettings } = buildContext(true, true)
+        const result = replaceLinks({
+            body: "My name is John",
+            linkResolverContext: { filePath: "test", trie, candidateMap },
+            settings: replaceSettings,
+        })
+        expect(result).toBe("[[My name]] is John")
+    })
+
+    it("handles path with alias (namespace)", () => {
+        const settings = {
+            scoped: false,
+            baseDir: undefined,
+            ignoreCase: false,
+        }
+        const { candidateMap, trie } = buildCandidateTrieForTest({
+            files: [{ path: "people/my name" }],
+            settings,
+        })
+        const result = replaceLinks({
+            body: "My name is here",
+            linkResolverContext: { filePath: "test", trie, candidateMap },
+            settings: { ...settings, matchSentenceCase: true, proximityBasedLinking: true },
+        })
+        expect(result).toBe("[[people/my name|My name]] is here")
+    })
+})

src/replace-links/__tests__/replace-links.table.test.ts

@@ -1,8 +1,13 @@
 import { describe, it, expect } from "vitest"
-import { replaceLinks } from "../replace-links"
+import { escapeLinkForMarkdownTable, replaceLinks } from "../replace-links"
 import { buildCandidateTrieForTest } from "./test-helpers"
 
 describe("table", () => {
+    it("escapes link separators only when rendering inside a markdown table", () => {
+        expect(escapeLinkForMarkdownTable("[[ns/note1|note1]]", true)).toBe("[[ns/note1\\|note1]]")
+        expect(escapeLinkForMarkdownTable("[[ns/note1|note1]]", false)).toBe("[[ns/note1|note1]]")
+    })
+
     it("escape pipe inside table", () => {
         const settings = {
             scoped: false,
@@ -32,6 +37,106 @@ describe("table", () => {
 | --------------------------------- | --- |
 | [[ns/note1\\|note1]]                             | |
 | [[ns/note2\\|note2]]                             | |
+`)
+    })
+
+    it("does not replace links inside tables when ignoreMarkdownTables is enabled", () => {
+        const settings = {
+            scoped: false,
+            baseDir: undefined,
+            proximityBasedLinking: true,
+        }
+        const { candidateMap, trie } = buildCandidateTrieForTest({
+            files: [{ path: "ns/note1" }],
+            settings,
+        })
+        const result = replaceLinks({
+            body: `
+note1
+| Test Item | |
+| --- | --- |
+| note1 | |
+`,
+            linkResolverContext: {
+                filePath: "journals/2022-01-01",
+                trie,
+                candidateMap,
+            },
+            settings: {
+                ...settings,
+                ignoreMarkdownTables: true,
+            },
+        })
+        expect(result).toBe(`
+[[ns/note1|note1]]
+| Test Item | |
+| --- | --- |
+| note1 | |
+`)
+    })
+
+    it("does not replace existing links inside tables when ignoreMarkdownTables is enabled", () => {
+        const settings = {
+            scoped: false,
+            baseDir: undefined,
+            proximityBasedLinking: true,
+        }
+        const { candidateMap, trie } = buildCandidateTrieForTest({
+            files: [{ path: "ns/note1" }],
+            settings,
+        })
+        const result = replaceLinks({
+            body: `
+[[note1]]
+| Test Item | |
+| --- | --- |
+| [[note1]] | |
+`,
+            linkResolverContext: {
+                filePath: "journals/2022-01-01",
+                trie,
+                candidateMap,
+            },
+            settings: {
+                ...settings,
+                ignoreMarkdownTables: true,
+            },
+            resolvedAmbiguities: new Map([["[[note1]]", "ns/note1|note1"]]),
+        })
+        expect(result).toBe(`
+[[ns/note1|note1]]
+| Test Item | |
+| --- | --- |
+| [[note1]] | |
+`)
+    })
+
+    it("escapes table aliases after earlier resolved wikilinks change segment offsets", () => {
+        const settings = {
+            scoped: false,
+            baseDir: undefined,
+            proximityBasedLinking: true,
+        }
+        const { candidateMap, trie } = buildCandidateTrieForTest({
+            files: [{ path: "ns/note1" }],
+            settings,
+        })
+        const result = replaceLinks({
+            body: `[[note1]]
+| note1 | |
+`,
+            linkResolverContext: {
+                filePath: "journals/2022-01-01",
+                trie,
+                candidateMap,
+            },
+            settings,
+            resolvedAmbiguities: new Map([
+                ["[[note1]]", "very/long/path/note1|note1"],
+            ]),
+        })
+        expect(result).toBe(`[[very/long/path/note1|note1]]
+| [[ns/note1\\|note1]] | |
 `)
     })
 })

src/replace-links/candidate-scanner.ts

@@ -0,0 +1,788 @@
+import { CandidateData, getTopLevelDirectoryName, TrieNode } from "../trie"
+import { RAW_URL_AT_START_PATTERN, RAW_URL_SOURCE } from "../markdown-protection"
+import { isMarkdownTableLine, segmentMarkdown } from "../markdown-segments"
+import type { ReplaceLinksSettings } from "./replace-links"
+
+export type CandidateOccurrenceKind = "unlinked" | "existing-wikilink"
+
+export interface CandidateOccurrence {
+    kind: CandidateOccurrenceKind
+    start: number
+    end: number
+    text: string
+    candidateKey: string
+    candidateData: CandidateData
+    replacementCandidateData?: CandidateData
+    isInTable: boolean
+}
+
+export type UnlinkedCandidateScanResult
+    = | { action: "match", occurrence: CandidateOccurrence }
+        | { action: "skip", end: number }
+        | null
+
+export interface ScanCandidateOccurrencesOptions {
+    text: string
+    filePath: string
+    trie: TrieNode
+    candidateMap: Map<string, CandidateData>
+    settings?: ReplaceLinksSettings
+}
+
+export const REGEX_PATTERNS = {
+    PROTECTED: new RegExp(
+        `(\`\`\`[\\s\\S]*?\`\`\`|\`[^\`]*\`|\\[\\[([^\\]]+)\\]\\]|\\[[^\\]]+\\]\\([^)]+\\)|\\[[^\\]]+\\]|${RAW_URL_SOURCE})`,
+        "g",
+    ),
+    DATE_FORMAT: /^\d{4}-\d{2}-\d{2}$/,
+    MONTH_NOTE: /^[0-9]{1,2}$/,
+    CJK: /[\p{Script=Han}\p{Script=Hiragana}\p{Script=Katakana}]/u,
+    CJK_CANDIDATE: /^[\p{Script=Han}\p{Script=Hiragana}\p{Script=Katakana}\p{Script=Hangul}\s\d]+$/u,
+    KOREAN: /^[\p{Script=Hangul}]+$/u,
+    JAPANESE: /^[\p{Script=Han}\p{Script=Hiragana}\p{Script=Katakana}\s\d]+$/u,
+    URL: RAW_URL_AT_START_PATTERN,
+    PROTECTED_LINK: /^\s*(\[\[[^\]]+\]\]|\[[^\]]+\]\([^)]+\))\s*$/,
+    KOREAN_SUFFIX: /^(이다\.?)/,
+    KOREAN_PARTICLES: /^(는|은)/,
+    KOREAN_PARTICLES_EXTENDED: /^(가|는|을|에|서|와|로부터|까지|보다|로|의|나|도|또한)/,
+    WORD_BOUNDARY: /[\p{L}\p{N}_/-]/u,
+    WHITESPACE: /[\t\n\r ]/,
+} as const
+
+export const isWordBoundary = (char: string | undefined): boolean => {
+    if (char === undefined) return true
+    if (REGEX_PATTERNS.CJK.test(char)) return true
+    return (!REGEX_PATTERNS.WORD_BOUNDARY.test(char) || REGEX_PATTERNS.WHITESPACE.test(char))
+}
+
+export const isMonthNote = (candidate: string): boolean =>
+    REGEX_PATTERNS.MONTH_NOTE.test(candidate)
+    && parseInt(candidate, 10) >= 1
+    && parseInt(candidate, 10) <= 12
+
+export const isProtectedLink = (body: string): boolean => REGEX_PATTERNS.PROTECTED_LINK.test(body)
+
+export const isCjkText = (text: string): boolean => REGEX_PATTERNS.CJK.test(text)
+
+export const isCjkCandidate = (candidate: string): boolean => REGEX_PATTERNS.CJK_CANDIDATE.test(candidate)
+
+export const isKoreanText = (text: string): boolean => REGEX_PATTERNS.KOREAN.test(text)
+
+export const isSentenceStart = (text: string, index: number): boolean => {
+    if (index === 0) return true
+    if (text[index - 1] === "\n") return true
+    if (index >= 3 && text[index - 1] === " " && text[index - 2] === ".") {
+        const charBeforePeriod = text[index - 3]
+        if (/[a-zA-Z]/.test(charBeforePeriod)) {
+            return true
+        }
+    }
+    return false
+}
+
+const fallbackIndexCache = new WeakMap<
+    Map<string, CandidateData>,
+    Map<string, Map<string, Array<[string, CandidateData]>>>
+>()
+
+export const buildFallbackIndex = (
+    candidateMap: Map<string, CandidateData>,
+    ignoreCase?: boolean,
+): Map<string, Array<[string, CandidateData]>> => {
+    let cacheForMap = fallbackIndexCache.get(candidateMap)
+    if (!cacheForMap) {
+        cacheForMap = new Map()
+        fallbackIndexCache.set(candidateMap, cacheForMap)
+    }
+
+    const cacheKey = ignoreCase ? "ignoreCase" : "normal"
+    const cached = cacheForMap.get(cacheKey)
+    if (cached) return cached
+
+    const fallbackIndex = new Map<string, Array<[string, CandidateData]>>()
+
+    for (const [key, data] of candidateMap.entries()) {
+        const slashIndex = key.lastIndexOf("/")
+        if (slashIndex === -1) continue
+
+        const shorthand = key.slice(slashIndex + 1)
+        const indexKey = ignoreCase ? shorthand.toLowerCase() : shorthand
+
+        let arr = fallbackIndex.get(indexKey)
+        if (!arr) {
+            arr = []
+            fallbackIndex.set(indexKey, arr)
+        }
+        arr.push([key, data])
+    }
+
+    cacheForMap.set(cacheKey, fallbackIndex)
+    return fallbackIndex
+}
+
+export const getCurrentNamespace = (filePath: string, baseDir?: string): string => {
+    if (baseDir) {
+        return getTopLevelDirectoryName(filePath, baseDir)
+    }
+
+    const segments = filePath.split("/")
+    return segments[0] || ""
+}
+
+export const normalizeCanonicalPath = (linkPath: string, baseDir?: string): string => {
+    if (baseDir && linkPath.startsWith(baseDir + "/")) {
+        return linkPath.slice((baseDir + "/").length)
+    }
+    return linkPath
+}
+
+export const extractLinkParts = (
+    canonicalPath: string,
+): { linkPath: string, alias: string, hasAlias: boolean } => {
+    const pipeIndex = canonicalPath.indexOf("|")
+    const hasAlias = pipeIndex !== -1
+
+    if (hasAlias) {
+        const linkPath = canonicalPath.slice(0, pipeIndex)
+        const alias = canonicalPath.slice(pipeIndex + 1)
+        return { linkPath, alias, hasAlias }
+    }
+
+    return { linkPath: canonicalPath, alias: "", hasAlias }
+}
+
+export const escapeRegExp = (text: string): string =>
+    text.replace(/[.*+?^${}()|[\]\\]/g, "\\$&")
+
+const findFencedCodeBlockRanges = (
+    body: string,
+): Array<{ start: number, end: number }> => {
+    if (!body.includes("```") && !body.includes("~~~")) {
+        return []
+    }
+
+    const ranges: Array<{ start: number, end: number }> = []
+    const openingFencePattern = /^ {0,3}(`{3,}|~{3,})[^\r\n]*(?:\r?\n|$)/gm
+    let openingMatch: RegExpExecArray | null
+
+    while ((openingMatch = openingFencePattern.exec(body)) !== null) {
+        const openingFence = openingMatch[1]
+        const fenceChar = openingFence[0]
+        const fenceLength = openingFence.length
+        const closingFencePattern = new RegExp(
+            `^ {0,3}${escapeRegExp(fenceChar)}{${fenceLength},}[ \\t]*(?:\\r?\\n|$)`,
+            "gm",
+        )
+        closingFencePattern.lastIndex = openingMatch.index + openingMatch[0].length
+        const closingMatch = closingFencePattern.exec(body)
+        const end = closingMatch
+            ? closingMatch.index + closingMatch[0].length
+            : body.length
+
+        ranges.push({
+            start: openingMatch.index,
+            end,
+        })
+        openingFencePattern.lastIndex = end
+    }
+
+    return ranges
+}
+
+export const extractFencedCodeBlocks = (
+    body: string,
+): { body: string, codeBlocks: Array<{ placeholder: string, content: string }> } => {
+    if (!body.includes("```") && !body.includes("~~~")) {
+        return { body, codeBlocks: [] }
+    }
+
+    const ranges = findFencedCodeBlockRanges(body)
+    const codeBlocks: Array<{ placeholder: string, content: string }> = []
+    let result = ""
+    let cursor = 0
+    for (const [codeBlockIndex, range] of ranges.entries()) {
+        const placeholder = `__CODE_BLOCK_${codeBlockIndex}__`
+        codeBlocks.push({
+            placeholder,
+            content: body.slice(range.start, range.end),
+        })
+        result += body.slice(cursor, range.start) + placeholder
+        cursor = range.end
+    }
+
+    result += body.slice(cursor)
+    return { body: result, codeBlocks }
+}
+
+export const isSelfLink = (
+    candidateData: CandidateData,
+    currentFilePath: string,
+    settings: ReplaceLinksSettings = {},
+): boolean => {
+    if (!settings.preventSelfLinking || candidateData.candidates.length === 0) {
+        return false
+    }
+
+    const { linkPath } = extractLinkParts(candidateData.candidates[0].canonical)
+    const normalizedLinkPath = normalizeCanonicalPath(
+        linkPath,
+        settings.baseDir,
+    )
+    const normalizedCurrentPath = normalizeCanonicalPath(
+        currentFilePath,
+        settings.baseDir,
+    )
+
+    return normalizedLinkPath === normalizedCurrentPath
+}
+
+export const shouldSkipCandidate = (
+    candidate: string,
+    settings: ReplaceLinksSettings,
+): boolean => {
+    if (
+        settings.ignoreDateFormats
+        && REGEX_PATTERNS.DATE_FORMAT.test(candidate)
+    ) {
+        return true
+    }
+    return isMonthNote(candidate)
+}
+
+export const isIndexInsideMarkdownTable = (text: string, index: number): boolean => {
+    let lineStart = text.lastIndexOf("\n", index - 1) + 1
+    if (lineStart === 0 && text[0] !== "\n") {
+        lineStart = 0
+    }
+
+    let lineEnd = text.indexOf("\n", index)
+    if (lineEnd === -1) {
+        lineEnd = text.length
+    }
+
+    const line = text.slice(lineStart, lineEnd)
+    return isMarkdownTableLine(line)
+}
+
+export const findBestCandidateInSameNamespace = (
+    filteredCandidates: Array<[string, CandidateData]>,
+    filePath: string,
+    settings: ReplaceLinksSettings = {},
+): [string, CandidateData] | null => {
+    let bestCandidate: [string, CandidateData] | null = null
+    let bestScore = -1
+
+    const filePathDir = filePath.includes("/")
+        ? filePath.slice(0, filePath.lastIndexOf("/"))
+        : ""
+    const filePathSegments = filePathDir ? filePathDir.split("/") : []
+
+    for (const [key, data] of filteredCandidates) {
+        const slashIndex = key.lastIndexOf("/")
+        const candidateDir = key.slice(0, slashIndex)
+        const candidateSegments = candidateDir.split("/")
+        let score = 0
+
+        for (
+            let idx = 0;
+            idx < Math.min(candidateSegments.length, filePathSegments.length);
+            idx++
+        ) {
+            if (candidateSegments[idx] === filePathSegments[idx]) {
+                score++
+            }
+            else {
+                break
+            }
+        }
+
+        if (score > bestScore) {
+            bestScore = score
+            bestCandidate = [key, data]
+        }
+        else if (score === bestScore && bestCandidate !== null) {
+            if (filePathDir === "" && settings.baseDir) {
+                const basePrefix = settings.baseDir + "/"
+                const getRelativeDepth = (k: string): number => {
+                    if (k.startsWith(basePrefix)) {
+                        const relativeParts = k
+                            .slice(basePrefix.length)
+                            .split("/")
+                        return relativeParts.length - 1
+                    }
+                    return Infinity
+                }
+
+                const candidateDepth = getRelativeDepth(key)
+                const bestCandidateDepth = getRelativeDepth(bestCandidate[0])
+
+                if (candidateDepth < bestCandidateDepth
+                    || (candidateDepth === bestCandidateDepth && key.length < bestCandidate[0].length)) {
+                    bestCandidate = [key, data]
+                }
+            }
+            else {
+                const currentBestDir = bestCandidate[0].slice(0, bestCandidate[0].lastIndexOf("/"))
+                const currentBestSegments = currentBestDir.split("/")
+
+                if (
+                    candidateSegments.length < currentBestSegments.length
+                    || (candidateSegments.length === currentBestSegments.length && key.length < bestCandidate[0].length)
+                ) {
+                    bestCandidate = [key, data]
+                }
+            }
+        }
+    }
+
+    return bestCandidate
+}
+
+const dedupeCandidates = (candidates: CandidateData["candidates"]): CandidateData => {
+    const unique = new Map(candidates.map(candidate => [candidate.canonical, candidate]))
+    return {
+        candidates: Array.from(unique.values()).sort((a, b) => {
+            if (a.canonical.length !== b.canonical.length) {
+                return a.canonical.length - b.canonical.length
+            }
+            return a.canonical.localeCompare(b.canonical)
+        }),
+    }
+}
+
+const collectExistingWikilinks = (
+    text: string,
+    segments: ReturnType<typeof segmentMarkdown>,
+    candidateMap: Map<string, CandidateData>,
+    occurrences: CandidateOccurrence[],
+    settings: ReplaceLinksSettings,
+): void => {
+    const existingLinkRegex = /^\[\[([^|\]]+)(?:\|([^\]]+))?\]\]$/
+
+    for (const segment of segments) {
+        if (segment.kind !== "protected" || segment.protectedKind !== "wikilink") {
+            continue
+        }
+
+        const match = segment.text.match(existingLinkRegex)
+        if (!match) {
+            continue
+        }
+
+        const fullMatch = match[0]
+        const path = match[1]
+        const alias = match[2] || path
+        const candidateKey = settings.ignoreCase ? alias.toLowerCase() : alias
+        const candidateData = candidateMap.get(candidateKey) ?? candidateMap.get(alias)
+
+        if (!candidateData) {
+            continue
+        }
+
+        occurrences.push({
+            kind: "existing-wikilink",
+            start: segment.start,
+            end: segment.end,
+            text: fullMatch,
+            candidateKey,
+            candidateData: dedupeCandidates(candidateData.candidates),
+            isInTable: isIndexInsideMarkdownTable(text, segment.start),
+        })
+    }
+}
+
+const collectFallbackOccurrence = ({
+    text,
+    startIndex,
+    fallbackIndex,
+    filePath,
+    currentNamespace,
+    settings,
+}: {
+    text: string
+    startIndex: number
+    fallbackIndex: Map<string, Array<[string, CandidateData]>>
+    filePath: string
+    currentNamespace: string
+    settings: ReplaceLinksSettings
+}): UnlinkedCandidateScanResult => {
+    const prevChar = text[startIndex - 1]
+    if (!isWordBoundary(prevChar)) {
+        return null
+    }
+
+    let longestMatch: {
+        word: string
+        length: number
+        key: string
+        candidateList: Array<[string, CandidateData]>
+    } | null = null
+
+    const maxSearchLength = Math.min(text.length - startIndex, 100)
+
+    let potentialMatch = ""
+    let searchWord = ""
+
+    for (let length = 1; length <= maxSearchLength; length++) {
+        const endIndex = startIndex + length
+        const currentChar = text[startIndex + length - 1]
+        potentialMatch += currentChar
+
+        if (settings.matchSentenceCase && !settings.ignoreCase && isSentenceStart(text, startIndex)) {
+            if (length === 1) {
+                searchWord = currentChar.toLowerCase()
+            }
+            else {
+                searchWord += currentChar
+            }
+        }
+        else {
+            searchWord = settings.ignoreCase
+                ? searchWord + currentChar.toLowerCase()
+                : potentialMatch
+        }
+
+        const candidateList = fallbackIndex.get(searchWord)
+        if (!candidateList) {
+            continue
+        }
+
+        const nextChar = text[endIndex]
+        if (!isWordBoundary(nextChar)) {
+            continue
+        }
+
+        if (shouldSkipCandidate(potentialMatch, settings)) {
+            continue
+        }
+
+        longestMatch = {
+            word: potentialMatch,
+            length,
+            key: searchWord,
+            candidateList,
+        }
+    }
+
+    if (!longestMatch) return null
+
+    const filteredCandidates = longestMatch.candidateList.filter(([, data]) => {
+        if (data.candidates.length === 0 || !settings.proximityBasedLinking) {
+            return true
+        }
+        const candidate = data.candidates[0]
+        return !(candidate.scoped && candidate.namespace !== currentNamespace)
+    })
+
+    if (filteredCandidates.length === 0) {
+        return null
+    }
+
+    const candidateData = dedupeCandidates(
+        filteredCandidates.flatMap(([, data]) => data.candidates),
+    )
+
+    if (candidateData.candidates.length === 0) {
+        return null
+    }
+
+    const bestCandidateResult = filteredCandidates.length > 1
+        ? findBestCandidateInSameNamespace(filteredCandidates, filePath, settings)
+        : filteredCandidates[0]
+    if (!bestCandidateResult) {
+        return null
+    }
+
+    if (isSelfLink(bestCandidateResult[1], filePath, settings)) {
+        return {
+            action: "skip",
+            end: startIndex + longestMatch.length,
+        }
+    }
+
+    return {
+        action: "match",
+        occurrence: {
+            kind: "unlinked",
+            start: startIndex,
+            end: startIndex + longestMatch.length,
+            text: longestMatch.word,
+            candidateKey: longestMatch.key,
+            candidateData,
+            replacementCandidateData: bestCandidateResult[1],
+            isInTable: isIndexInsideMarkdownTable(text, startIndex),
+        },
+    }
+}
+
+const shouldSkipKoreanTrieOccurrence = (
+    text: string,
+    startIndex: number,
+    candidate: string,
+): boolean => {
+    if (!isKoreanText(candidate)) {
+        return false
+    }
+
+    const remaining = text.slice(startIndex + candidate.length)
+    return REGEX_PATTERNS.KOREAN_PARTICLES.test(remaining)
+}
+
+export const scanUnlinkedCandidateAt = ({
+    text,
+    startIndex,
+    filePath,
+    trie,
+    candidateMap,
+    fallbackIndex,
+    currentNamespace,
+    settings,
+}: {
+    text: string
+    startIndex: number
+    filePath: string
+    trie: TrieNode
+    candidateMap: Map<string, CandidateData>
+    fallbackIndex: Map<string, Array<[string, CandidateData]>>
+    currentNamespace: string
+    settings: ReplaceLinksSettings
+}): UnlinkedCandidateScanResult => {
+    if (
+        (text[startIndex] === "h" && text.slice(startIndex, startIndex + 4) === "http")
+        || (text[startIndex] === "l" && text.slice(startIndex, startIndex + 9) === "linear://")
+    ) {
+        const urlMatch = text.slice(startIndex).match(REGEX_PATTERNS.URL)
+        if (urlMatch) {
+            return {
+                action: "skip",
+                end: startIndex + urlMatch[0].length,
+            }
+        }
+    }
+
+    let node = trie
+    let lastCandidate: { candidate: string, length: number } | null = null
+    let j = startIndex
+    let candidateBuilder = ""
+
+    while (j < text.length) {
+        const ch = text[j]
+        let chLower = settings.ignoreCase ? ch.toLowerCase() : ch
+        if (settings.matchSentenceCase && !settings.ignoreCase && j === startIndex && isSentenceStart(text, startIndex)) {
+            chLower = ch.toLowerCase()
+        }
+        candidateBuilder += ch
+
+        const child = node.children.get(chLower)
+        if (!child) break
+
+        node = child
+        if (node.candidate) {
+            const candidateIsCjk = isCjkCandidate(candidateBuilder)
+            if (candidateIsCjk || isWordBoundary(text[j + 1])) {
+                lastCandidate = {
+                    candidate: node.candidate,
+                    length: j - startIndex + 1,
+                }
+            }
+        }
+        j++
+    }
+
+    if (lastCandidate) {
+        const candidate = candidateBuilder.slice(0, lastCandidate.length)
+
+        if (shouldSkipCandidate(candidate, settings)) {
+            return {
+                action: "skip",
+                end: startIndex + lastCandidate.length,
+            }
+        }
+
+        const trieCandidateKey = lastCandidate.candidate
+        const candidateData = candidateMap.get(trieCandidateKey)
+
+        if (candidateData) {
+            if (isSelfLink(candidateData, filePath, settings)) {
+                return {
+                    action: "skip",
+                    end: startIndex + candidate.length,
+                }
+            }
+
+            if (shouldSkipKoreanTrieOccurrence(text, startIndex, candidate)) {
+                return {
+                    action: "skip",
+                    end: startIndex + 1,
+                }
+            }
+
+            const candidateIsCjk = isCjkCandidate(candidate)
+            if (!candidateIsCjk) {
+                const left = startIndex > 0 ? text[startIndex - 1] : undefined
+                const right = startIndex + candidate.length < text.length
+                    ? text[startIndex + candidate.length]
+                    : undefined
+
+                if (!isWordBoundary(left) || !isWordBoundary(right)) {
+                    return {
+                        action: "skip",
+                        end: startIndex + 1,
+                    }
+                }
+            }
+
+            if (
+                settings.proximityBasedLinking
+                && candidateData.candidates.length > 0
+                && candidateData.candidates[0].scoped
+                && candidateData.candidates[0].namespace !== currentNamespace
+            ) {
+                return {
+                    action: "skip",
+                    end: startIndex + candidate.length,
+                }
+            }
+
+            return {
+                action: "match",
+                occurrence: {
+                    kind: "unlinked",
+                    start: startIndex,
+                    end: startIndex + candidate.length,
+                    text: candidate,
+                    candidateKey: trieCandidateKey,
+                    candidateData: dedupeCandidates(candidateData.candidates),
+                    replacementCandidateData: candidateData,
+                    isInTable: isIndexInsideMarkdownTable(text, startIndex),
+                },
+            }
+        }
+    }
+
+    if (settings.proximityBasedLinking) {
+        return collectFallbackOccurrence({
+            text,
+            startIndex,
+            fallbackIndex,
+            filePath,
+            currentNamespace,
+            settings,
+        })
+    }
+
+    return null
+}
+
+const collectUnlinkedOccurrences = ({
+    text,
+    filePath,
+    trie,
+    candidateMap,
+    fallbackIndex,
+    currentNamespace,
+    settings,
+    occurrences,
+}: {
+    text: string
+    filePath: string
+    trie: TrieNode
+    candidateMap: Map<string, CandidateData>
+    fallbackIndex: Map<string, Array<[string, CandidateData]>>
+    currentNamespace: string
+    settings: ReplaceLinksSettings
+    occurrences: CandidateOccurrence[]
+}): void => {
+    let i = 0
+
+    while (i < text.length) {
+        const result = scanUnlinkedCandidateAt({
+            text,
+            startIndex: i,
+            filePath,
+            trie,
+            candidateMap,
+            fallbackIndex,
+            currentNamespace,
+            settings,
+        })
+
+        if (result?.action === "match") {
+            occurrences.push(result.occurrence)
+            i = result.occurrence.end
+            continue
+        }
+
+        if (result?.action === "skip") {
+            i = result.end
+            continue
+        }
+
+        i++
+    }
+}
+
+export const scanCandidateOccurrences = ({
+    text,
+    filePath,
+    trie,
+    candidateMap,
+    settings = {},
+}: ScanCandidateOccurrencesOptions): CandidateOccurrence[] => {
+    const occurrences: CandidateOccurrence[] = []
+    const normalizedText = text.normalize("NFC")
+    const fallbackIndex = buildFallbackIndex(candidateMap, settings.ignoreCase)
+    const currentNamespace = getCurrentNamespace(filePath, settings.baseDir)
+    const markdownSegments = segmentMarkdown(normalizedText, {
+        protectHeadings: settings.ignoreHeadings,
+        protectCallouts: true,
+        protectTableRows: settings.ignoreMarkdownTables,
+        protectUrls: true,
+    })
+
+    collectExistingWikilinks(
+        normalizedText,
+        markdownSegments,
+        candidateMap,
+        occurrences,
+        settings,
+    )
+
+    for (const segment of markdownSegments) {
+        if (segment.kind !== "prose") {
+            continue
+        }
+
+        const segmentOccurrences: CandidateOccurrence[] = []
+        collectUnlinkedOccurrences({
+            text: segment.text,
+            filePath,
+            trie,
+            candidateMap,
+            fallbackIndex,
+            currentNamespace,
+            settings,
+            occurrences: segmentOccurrences,
+        })
+
+        for (const occurrence of segmentOccurrences) {
+            occurrences.push({
+                ...occurrence,
+                start: occurrence.start + segment.start,
+                end: occurrence.end + segment.start,
+            })
+        }
+    }
+
+    return occurrences.sort((a, b) => a.start - b.start)
+}
+
+export const getOccurrenceContext = (
+    text: string,
+    occurrence: CandidateOccurrence,
+    maxContext: number,
+): string => {
+    const start = Math.max(0, occurrence.start - maxContext)
+    const end = Math.min(text.length, occurrence.end + maxContext)
+    return text.slice(start, end)
+}

src/replace-links/replace-links.ts

@@ -1,4 +1,15 @@
-import { CandidateData, getTopLevelDirectoryName, TrieNode } from "../trie"
+import { CandidateData, TrieNode } from "../trie"
+import { mapMarkdownProse, segmentMarkdown } from "../markdown-segments"
+import {
+    buildFallbackIndex,
+    extractLinkParts,
+    getCurrentNamespace,
+    isCjkText,
+    isIndexInsideMarkdownTable,
+    isProtectedLink,
+    normalizeCanonicalPath,
+    scanUnlinkedCandidateAt,
+} from "./candidate-scanner"
 
 // Types for the replaceLinks function
 export interface LinkResolverContext {
@@ -12,8 +23,11 @@ export interface ReplaceLinksSettings {
     baseDir?: string
     ignoreDateFormats?: boolean
     ignoreCase?: boolean
+    matchSentenceCase?: boolean
     preventSelfLinking?: boolean
     removeAliasInDirs?: string[]
+    ignoreHeadings?: boolean
+    ignoreMarkdownTables?: boolean
 }
 
 export interface LinkGeneratorParams {
@@ -30,159 +44,7 @@ export interface ReplaceLinksOptions {
     linkResolverContext: LinkResolverContext
     settings?: ReplaceLinksSettings
     linkGenerator?: LinkGenerator
-}
-
-// Constants and Regular Expressions
-const REGEX_PATTERNS = {
-    PROTECTED: /(```[\s\S]*?```|`[^`]*`|\[\[[^\]]+\]\]|\[[^\]]+\]\([^)]+\)|\[[^\]]+\]|https?:\/\/[^\s]+)/g,
-    DATE_FORMAT: /^\d{4}-\d{2}-\d{2}$/,
-    MONTH_NOTE: /^[0-9]{1,2}$/,
-    CJK: /[\p{Script=Han}\p{Script=Hiragana}\p{Script=Katakana}]/u,
-    CJK_CANDIDATE: /^[\p{Script=Han}\p{Script=Hiragana}\p{Script=Katakana}\p{Script=Hangul}\s\d]+$/u,
-    KOREAN: /^[\p{Script=Hangul}]+$/u,
-    JAPANESE: /^[\p{Script=Han}\p{Script=Hiragana}\p{Script=Katakana}\s\d]+$/u,
-    URL: /^(https?:\/\/[^\s]+)/,
-    PROTECTED_LINK: /^\s*(\[\[[^\]]+\]\]|\[[^\]]+\]\([^)]+\))\s*$/,
-    KOREAN_SUFFIX: /^(이다\.?)/,
-    KOREAN_PARTICLES: /^(는|은)/,
-    JAPANESE_PARTICLES: /^(가|는|을|에|서|와|로부터|까지|보다|로|의|나|도|또한)/,
-    TABLE_SEPARATOR: /^[|:\s-]+$/,
-    WORD_BOUNDARY: /[\p{L}\p{N}_/-]/u,
-    WHITESPACE: /[\t\n\r ]/,
-} as const
-
-// Text Analysis Utilities
-const isWordBoundary = (char: string | undefined): boolean => {
-    if (char === undefined) return true
-    if (REGEX_PATTERNS.CJK.test(char)) return true
-    return (
-        !REGEX_PATTERNS.WORD_BOUNDARY.test(char)
-        || REGEX_PATTERNS.WHITESPACE.test(char)
-    )
-}
-
-const isMonthNote = (candidate: string): boolean =>
-    REGEX_PATTERNS.MONTH_NOTE.test(candidate)
-    && parseInt(candidate, 10) >= 1
-    && parseInt(candidate, 10) <= 12
-
-const isProtectedLink = (body: string): boolean =>
-    REGEX_PATTERNS.PROTECTED_LINK.test(body)
-
-const isCjkText = (text: string): boolean => REGEX_PATTERNS.CJK.test(text)
-
-const isCjkCandidate = (candidate: string): boolean =>
-    REGEX_PATTERNS.CJK_CANDIDATE.test(candidate)
-
-const isKoreanText = (text: string): boolean =>
-    REGEX_PATTERNS.KOREAN.test(text)
-
-const isJapaneseText = (text: string): boolean =>
-    REGEX_PATTERNS.JAPANESE.test(text) && !REGEX_PATTERNS.KOREAN.test(text)
-
-// Cache for fallback index to avoid rebuilding
-const fallbackIndexCache = new WeakMap<
-    Map<string, CandidateData>,
-    Map<string, Map<string, Array<[string, CandidateData]>>>
->()
-
-const buildFallbackIndex = (
-    candidateMap: Map<string, CandidateData>,
-    ignoreCase?: boolean,
-): Map<string, Array<[string, CandidateData]>> => {
-    // Get or create cache for this candidateMap
-    let cacheForMap = fallbackIndexCache.get(candidateMap)
-    if (!cacheForMap) {
-        cacheForMap = new Map()
-        fallbackIndexCache.set(candidateMap, cacheForMap)
-    }
-
-    // Check if we have cached result for this ignoreCase setting
-    const cacheKey = ignoreCase ? "ignoreCase" : "normal"
-    const cached = cacheForMap.get(cacheKey)
-    if (cached) {
-        return cached
-    }
-
-    // Build new fallback index
-    const fallbackIndex = new Map<string, Array<[string, CandidateData]>>()
-
-    for (const [key, data] of candidateMap.entries()) {
-        const slashIndex = key.lastIndexOf("/")
-        if (slashIndex === -1) continue
-
-        const shorthand = key.slice(slashIndex + 1)
-        const indexKey = ignoreCase ? shorthand.toLowerCase() : shorthand
-
-        let arr = fallbackIndex.get(indexKey)
-        if (!arr) {
-            arr = []
-            fallbackIndex.set(indexKey, arr)
-        }
-        arr.push([key, data])
-    }
-
-    // Cache the result
-    cacheForMap.set(cacheKey, fallbackIndex)
-    return fallbackIndex
-}
-
-const getCurrentNamespace = (filePath: string, baseDir?: string): string => {
-    if (baseDir) {
-        return getTopLevelDirectoryName(filePath, baseDir)
-    }
-
-    const segments = filePath.split("/")
-    return segments[0] || ""
-}
-
-const normalizeCanonicalPath = (linkPath: string, baseDir?: string): string => {
-    if (baseDir && linkPath.startsWith(baseDir + "/")) {
-        return linkPath.slice((baseDir + "/").length)
-    }
-    return linkPath
-}
-
-const extractLinkParts = (
-    canonicalPath: string,
-): { linkPath: string, alias: string, hasAlias: boolean } => {
-    const pipeIndex = canonicalPath.indexOf("|")
-    const hasAlias = pipeIndex !== -1
-
-    if (hasAlias) {
-        const linkPath = canonicalPath.slice(0, pipeIndex)
-        const alias = canonicalPath.slice(pipeIndex + 1)
-        return { linkPath, alias, hasAlias }
-    }
-
-    return { linkPath: canonicalPath, alias: "", hasAlias }
-}
-
-// Self-linking Prevention
-const isSelfLink = (
-    candidateData: CandidateData,
-    currentFilePath: string,
-    settings: ReplaceLinksSettings = {},
-): boolean => {
-    if (!settings.preventSelfLinking) {
-        return false
-    }
-
-    // Extract the link path from the canonical path
-    const { linkPath } = extractLinkParts(candidateData.canonical)
-
-    // Normalize paths for comparison
-    const normalizedLinkPath = normalizeCanonicalPath(
-        linkPath,
-        settings.baseDir,
-    )
-    const normalizedCurrentPath = normalizeCanonicalPath(
-        currentFilePath,
-        settings.baseDir,
-    )
-
-    // Compare the paths
-    return normalizedLinkPath === normalizedCurrentPath
+    resolvedAmbiguities?: Map<string, string>
 }
 
 // Helper function to check if a path should have its alias removed
@@ -215,8 +77,11 @@ const createLinkContent = (
     originalMatchedText: string,
     settings: ReplaceLinksSettings = {},
 ): { linkPath: string, alias?: string } => {
+    if (candidateData.candidates.length === 0) {
+        return { linkPath: originalMatchedText }
+    }
     const { linkPath, alias, hasAlias } = extractLinkParts(
-        candidateData.canonical,
+        candidateData.candidates[0].canonical,
     )
     const normalizedPath = normalizeCanonicalPath(linkPath, settings.baseDir)
 
@@ -231,8 +96,8 @@ const createLinkContent = (
         if (removeAlias) {
             return { linkPath: normalizedPath }
         }
-        // Use originalMatchedText to preserve case when ignoreCase is enabled
-        const displayAlias = settings.ignoreCase ? originalMatchedText : alias
+        // Use originalMatchedText to preserve case when ignoreCase or matchSentenceCase is enabled
+        const displayAlias = (settings.ignoreCase || settings.matchSentenceCase) ? originalMatchedText : alias
         return { linkPath: normalizedPath, alias: displayAlias }
     }
 
@@ -243,19 +108,18 @@ const createLinkContent = (
         }
 
         // For paths with slashes, use the last segment as the display text
-        const lastSegment
-            = normalizedPath.split("/").pop() || originalMatchedText
+        const lastSegment = normalizedPath.split("/").pop() || originalMatchedText
 
         // If ignoreCase is enabled and originalMatchedText contains a slash,
         // use the last segment of originalMatchedText to preserve case
         let displayText = lastSegment
-        if (settings.ignoreCase && originalMatchedText.includes("/")) {
+        if ((settings.ignoreCase || settings.matchSentenceCase) && originalMatchedText.includes("/")) {
             const originalLastSegment = originalMatchedText.split("/").pop()
             if (originalLastSegment) {
                 displayText = originalLastSegment
             }
         }
-        else if (settings.ignoreCase) {
+        else if (settings.ignoreCase || settings.matchSentenceCase) {
             // If originalMatchedText doesn't contain a slash, use it as-is
             displayText = originalMatchedText
         }
@@ -284,7 +148,36 @@ const createLinkContent = (
     }
 }
 
+const resolveLinkContent = (
+    candidateData: CandidateData,
+    originalMatchedText: string,
+    settings: ReplaceLinksSettings,
+    resolvedAmbiguities?: Map<string, string>,
+): { linkPath: string, alias?: string } => {
+    if (resolvedAmbiguities?.has(originalMatchedText)) {
+        const resolvedPath = resolvedAmbiguities.get(originalMatchedText)!
+        const parts = extractLinkParts(resolvedPath)
+        return {
+            linkPath: parts.linkPath,
+            alias: parts.alias || originalMatchedText,
+        }
+    }
+
+    return createLinkContent(candidateData, originalMatchedText, settings)
+}
+
 // Default link generator that creates standard Obsidian wikilinks
+export const escapeLinkForMarkdownTable = (
+    link: string,
+    isInTable = false,
+): string => {
+    if (isInTable && link.includes("|")) {
+        return link.replace(/\|/g, "\\|")
+    }
+
+    return link
+}
+
 export const defaultLinkGenerator: LinkGenerator = ({
     linkPath,
     alias,
@@ -296,61 +189,7 @@ export const defaultLinkGenerator: LinkGenerator = ({
         linkContent = `${linkPath}|${alias}`
     }
 
-    if (isInTable && linkContent.includes("|")) {
-        linkContent = linkContent.replace(/\|/g, "\\|")
-    }
-
-    return `[[${linkContent}]]`
-}
-
-// Candidate Validation
-const shouldSkipCandidate = (
-    candidate: string,
-    settings: ReplaceLinksSettings,
-): boolean => {
-    if (
-        settings.ignoreDateFormats
-        && REGEX_PATTERNS.DATE_FORMAT.test(candidate)
-    ) {
-        return true
-    }
-    return isMonthNote(candidate)
-}
-
-// Markdown Table Detection
-const isMarkdownTableLine = (line: string): boolean => {
-    const trimmedLine = line.trim()
-    if (!trimmedLine || !trimmedLine.includes("|")) {
-        return false
-    }
-
-    if (
-        trimmedLine.startsWith("|")
-        && trimmedLine.endsWith("|")
-        && REGEX_PATTERNS.TABLE_SEPARATOR.test(trimmedLine)
-    ) {
-        return true
-    }
-
-    return trimmedLine.startsWith("|") && trimmedLine.endsWith("|")
-}
-
-const isIndexInsideMarkdownTable = (text: string, index: number): boolean => {
-    // Find the start of the line containing the index
-    let lineStart = text.lastIndexOf("\n", index - 1) + 1
-    if (lineStart === 0 && text[0] !== "\n") {
-        lineStart = 0
-    }
-
-    // Find the end of the line containing the index
-    let lineEnd = text.indexOf("\n", index)
-    if (lineEnd === -1) {
-        lineEnd = text.length
-    }
-
-    // Extract the line and check if it's a table line
-    const line = text.slice(lineStart, lineEnd)
-    return isMarkdownTableLine(line)
+    return escapeLinkForMarkdownTable(`[[${linkContent}]]`, isInTable)
 }
 
 // Processing functions for different text types
@@ -362,6 +201,8 @@ const processCjkText = (
     filePath: string,
     linkGenerator: LinkGenerator,
     settings: ReplaceLinksSettings = {},
+    resolvedAmbiguities?: Map<string, string>,
+    forceIsInTable?: boolean,
 ): string => {
     // For CJK texts that might contain non-CJK terms like "taro-san", ensure we use a consistent approach
     // Pass the proper filePath to maintain correct namespace resolution
@@ -374,266 +215,11 @@ const processCjkText = (
         currentNamespace,
         linkGenerator,
         settings,
+        resolvedAmbiguities,
+        forceIsInTable,
     )
 }
 
-// Fallback Search Processing
-const processFallbackSearch = (
-    text: string,
-    startIndex: number,
-    fallbackIndex: Map<string, Array<[string, CandidateData]>>,
-    filePath: string,
-    currentNamespace: string,
-    linkGenerator: LinkGenerator,
-    settings: ReplaceLinksSettings,
-): { result: string, newIndex: number } | null => {
-    // Early boundary check - if start isn't a word boundary, skip
-    const prevChar = text[startIndex - 1]
-    if (!isWordBoundary(prevChar)) {
-        return null
-    }
-
-    let longestMatch: {
-        word: string
-        length: number
-        key: string
-        candidateList: Array<[string, CandidateData]>
-    } | null = null
-
-    // Iterate through potential multi-word sequences starting from startIndex
-    const maxSearchLength = Math.min(text.length - startIndex, 100) // Limit search length for performance
-
-    let potentialMatch = ""
-    let searchWord = ""
-
-    for (let length = 1; length <= maxSearchLength; length++) {
-        const endIndex = startIndex + length
-        const currentChar = text[startIndex + length - 1]
-        potentialMatch += currentChar
-        searchWord = settings.ignoreCase
-            ? searchWord + currentChar.toLowerCase()
-            : potentialMatch
-
-        // Check if this potential match exists in fallback index
-        const candidateList = fallbackIndex.get(searchWord)
-        if (!candidateList) {
-            continue
-        }
-
-        // Basic boundary check: next char should be a boundary if not end of text
-        const nextChar = text[endIndex]
-        if (!isWordBoundary(nextChar)) {
-            continue // This isn't a valid match end
-        }
-
-        // Skip date formats and month notes
-        if (shouldSkipCandidate(potentialMatch, settings)) {
-            continue // Try longer match
-        }
-
-        // Found a valid candidate
-        longestMatch = {
-            word: potentialMatch,
-            length: length,
-            key: searchWord,
-            candidateList: candidateList,
-        }
-        // Continue checking for even longer matches
-    }
-
-    // Process the longest valid match found
-    if (!longestMatch) return null
-
-    // Filter candidates based on namespace restrictions
-    const filteredCandidates = longestMatch.candidateList.filter(
-        ([, data]) => !(data.scoped && data.namespace !== currentNamespace),
-    )
-
-    let bestCandidateData: CandidateData | null = null
-
-    if (filteredCandidates.length === 1) {
-        bestCandidateData = filteredCandidates[0][1]
-    }
-    else if (filteredCandidates.length > 1) {
-        const bestCandidateResult = findBestCandidateInSameNamespace(
-            filteredCandidates,
-            filePath,
-            settings,
-        )
-        if (bestCandidateResult) {
-            bestCandidateData = bestCandidateResult[1]
-        }
-    }
-
-    if (!bestCandidateData) return null
-
-    // Check if this is a self-link and should be prevented
-    if (isSelfLink(bestCandidateData, filePath, settings)) {
-        return {
-            result: longestMatch.word,
-            newIndex: startIndex + longestMatch.length,
-        }
-    }
-
-    // Create the link
-    const { linkPath, alias } = createLinkContent(
-        bestCandidateData,
-        longestMatch.word,
-        settings,
-    )
-    const isInTable = isIndexInsideMarkdownTable(text, startIndex)
-    const finalLink = linkGenerator({
-        linkPath,
-        sourcePath: filePath,
-        alias,
-        isInTable,
-    })
-
-    return {
-        result: finalLink,
-        newIndex: startIndex + longestMatch.length,
-    }
-}
-
-// Korean Language Processing
-const handleKoreanSpecialCases = (
-    text: string,
-    i: number,
-    candidate: string,
-    candidateData: CandidateData,
-    filePath: string,
-    linkGenerator: LinkGenerator,
-    settings: ReplaceLinksSettings = {},
-): { result: string, newIndex: number } | null => {
-    const remaining = text.slice(i + candidate.length)
-
-    // Special handling when followed by "이다"
-    const suffixMatch = remaining.match(REGEX_PATTERNS.KOREAN_SUFFIX)
-    if (suffixMatch) {
-        // Check if this is a self-link and should be prevented
-        if (isSelfLink(candidateData, filePath, settings)) {
-            return {
-                result: candidate + suffixMatch[0],
-                newIndex: i + candidate.length + suffixMatch[0].length,
-            }
-        }
-
-        const { linkPath, alias } = createLinkContent(
-            candidateData,
-            candidate,
-            settings,
-        )
-        const finalLink = linkGenerator({
-            linkPath,
-            sourcePath: filePath,
-            alias,
-            isInTable: false,
-        })
-
-        return {
-            result: finalLink + suffixMatch[0],
-            newIndex: i + candidate.length + suffixMatch[0].length,
-        }
-    }
-
-    // Special handling when followed by particles like "는" or "은"
-    if (remaining.match(REGEX_PATTERNS.KOREAN_PARTICLES)) {
-        return {
-            result: text[i],
-            newIndex: i + 1,
-        }
-    }
-
-    return null
-}
-
-const findBestCandidateInSameNamespace = (
-    filteredCandidates: Array<[string, CandidateData]>,
-    filePath: string,
-    settings: ReplaceLinksSettings = {},
-): [string, CandidateData] | null => {
-    let bestCandidate: [string, CandidateData] | null = null
-    let bestScore = -1
-
-    // Get the directory portion of the current file (if any)
-    const filePathDir = filePath.includes("/")
-        ? filePath.slice(0, filePath.lastIndexOf("/"))
-        : ""
-    const filePathSegments = filePathDir ? filePathDir.split("/") : []
-
-    for (const [key, data] of filteredCandidates) {
-        const slashIndex = key.lastIndexOf("/")
-        const candidateDir = key.slice(0, slashIndex)
-        const candidateSegments = candidateDir.split("/")
-        let score = 0
-
-        // Calculate common prefix score
-        for (
-            let idx = 0;
-            idx < Math.min(candidateSegments.length, filePathSegments.length);
-            idx++
-        ) {
-            if (candidateSegments[idx] === filePathSegments[idx]) {
-                score++
-            }
-            else {
-                break
-            }
-        }
-
-        if (score > bestScore) {
-            bestScore = score
-            bestCandidate = [key, data]
-        }
-        else if (score === bestScore && bestCandidate !== null) {
-            if (filePathDir === "" && settings.baseDir) {
-                // When the current file is in the base directory, compare candidates by relative depth
-                const basePrefix = settings.baseDir + "/"
-                const getRelativeDepth = (k: string): number => {
-                    if (k.startsWith(basePrefix)) {
-                        // Remove the baseDir part and count the remaining segments
-                        const relativeParts = k
-                            .slice(basePrefix.length)
-                            .split("/")
-                        return relativeParts.length - 1
-                    }
-                    return Infinity
-                }
-
-                const candidateDepth = getRelativeDepth(key)
-                const bestCandidateDepth = getRelativeDepth(bestCandidate[0])
-
-                // Prefer the candidate with lower depth or shorter path
-                if (
-                    candidateDepth < bestCandidateDepth
-                    || (candidateDepth === bestCandidateDepth
-                        && key.length < bestCandidate[0].length)
-                ) {
-                    bestCandidate = [key, data]
-                }
-            }
-            else {
-                // Otherwise, choose the candidate with fewer directory segments
-                const currentBestDir = bestCandidate[0].slice(
-                    0,
-                    bestCandidate[0].lastIndexOf("/"),
-                )
-                const currentBestSegments = currentBestDir.split("/")
-
-                if (
-                    candidateSegments.length < currentBestSegments.length
-                    || (candidateSegments.length === currentBestSegments.length
-                        && key.length < bestCandidate[0].length)
-                ) {
-                    bestCandidate = [key, data]
-                }
-            }
-        }
-    }
-
-    return bestCandidate
-}
-
 const processStandardText = (
     text: string,
     trie: TrieNode,
@@ -643,192 +229,51 @@ const processStandardText = (
     currentNamespace: string,
     linkGenerator: LinkGenerator,
     settings: ReplaceLinksSettings = {},
+    resolvedAmbiguities?: Map<string, string>,
+    forceIsInTable?: boolean,
 ): string => {
     let result = ""
     let i = 0
 
-    outer: while (i < text.length) {
-        // Check for URLs first - only if current character could start a URL
-        if (text[i] === "h" && text.slice(i, i + 4) === "http") {
-            const urlMatch = text.slice(i).match(REGEX_PATTERNS.URL)
-            if (urlMatch) {
-                result += urlMatch[0]
-                i += urlMatch[0].length
-                continue
-            }
+    while (i < text.length) {
+        const scanResult = scanUnlinkedCandidateAt({
+            text,
+            startIndex: i,
+            filePath,
+            trie,
+            candidateMap,
+            fallbackIndex,
+            currentNamespace,
+            settings,
+        })
+
+        if (scanResult?.action === "skip") {
+            result += text.slice(i, scanResult.end)
+            i = scanResult.end
+            continue
         }
 
-        // Try to find a candidate using the trie
-        let node = trie
-        let lastCandidate: { candidate: string, length: number } | null = null
-        let j = i
-        let candidateBuilder = ""
-
-        while (j < text.length) {
-            const ch = text[j]
-            const chLower = settings.ignoreCase ? ch.toLowerCase() : ch
-            candidateBuilder += ch
-
-            const child = node.children.get(chLower)
-            if (!child) break
-
-            node = child
-            if (node.candidate) {
-                const candidateIsCjk = isCjkCandidate(candidateBuilder)
-
-                if (candidateIsCjk || isWordBoundary(text[j + 1])) {
-                    lastCandidate = {
-                        candidate: node.candidate,
-                        length: j - i + 1,
-                    }
-                }
-            }
-            j++
-        }
-
-        if (lastCandidate) {
-            const candidate = candidateBuilder.slice(0, lastCandidate.length)
-
-            // Skip if it's a date format
-            if (
-                settings.ignoreDateFormats
-                && REGEX_PATTERNS.DATE_FORMAT.test(candidate)
-            ) {
-                result += candidate
-                i += lastCandidate.length
-                continue outer
-            }
-
-            // Skip month notes
-            if (isMonthNote(candidate)) {
-                result += candidate
-                i += lastCandidate.length
-                continue
-            }
-
-            // Use the candidate found in the trie (lastCandidate.candidate) to look up in candidateMap
-            const trieCandidateKey = lastCandidate.candidate
-
-            // candidateMap lookup should always use the exact key from the trie result.
-            // Case comparison happened during trie traversal if ignoreCase is true.
-            const candidateData = candidateMap.get(trieCandidateKey)
-
-            // Store the original text matched for potential use as display text
-            const originalMatchedText = text.substring(
-                i,
-                i + lastCandidate.length,
-            )
-
-            if (candidateData) {
-                // Check if this is a self-link and should be prevented
-                if (isSelfLink(candidateData, filePath, settings)) {
-                    result += candidate
-                    i += candidate.length
-                    continue outer
-                }
-
-                // Handle Korean special cases
-                const isKorean = isKoreanText(candidate)
-                if (isKorean) {
-                    const koreanResult = handleKoreanSpecialCases(
-                        text,
-                        i,
-                        candidate,
-                        candidateData,
-                        filePath,
-                        linkGenerator,
-                        settings,
-                    )
-                    if (koreanResult) {
-                        result += koreanResult.result
-                        i = koreanResult.newIndex
-                        continue outer
-                    }
-                }
-
-                // Word boundary check for non-CJK text
-                const candidateIsCjk = isCjkCandidate(candidate)
-                if (!candidateIsCjk) {
-                    const left = i > 0 ? text[i - 1] : undefined
-                    const right
-                        = i + candidate.length < text.length
-                            ? text[i + candidate.length]
-                            : undefined
-
-                    if (!isWordBoundary(left) || !isWordBoundary(right)) {
-                        result += text[i]
-                        i++
-                        continue outer
-                    }
-                }
-
-                // Check for Japanese particles
-                const isJapaneseCandidate = isJapaneseText(candidate)
-                if (isJapaneseCandidate) {
-                    const right
-                        = i + candidate.length < text.length
-                            ? text.slice(
-                                    i + candidate.length,
-                                    i + candidate.length + 10,
-                                )
-                            : ""
-
-                    // Check for Japanese particles (no action needed, just a check point)
-                    if (right.match(REGEX_PATTERNS.JAPANESE_PARTICLES)) {
-                        // Skip word boundary check for Japanese particles
-                    }
-                }
-
-                // Skip if namespace restriction applies
-                if (
-                    settings.proximityBasedLinking
-                    && candidateData.scoped
-                    && candidateData.namespace !== currentNamespace
-                ) {
-                    result += candidate
-                    i += candidate.length
-                    continue outer
-                }
-
-                // Create the link
-                const { linkPath, alias } = createLinkContent(
-                    candidateData,
-                    originalMatchedText,
-                    settings,
-                )
-                const isInTable = isIndexInsideMarkdownTable(text, i)
-                const finalLink = linkGenerator({
-                    linkPath,
-                    sourcePath: filePath,
-                    alias,
-                    isInTable,
-                })
-                result += finalLink
-
-                i += candidate.length
-                continue outer
-            }
-        }
-
-        // Fallback: multi-word lookup using fallback index
-        if (settings.proximityBasedLinking) {
-            const fallbackResult = processFallbackSearch(
-                text,
-                i,
-                fallbackIndex,
-                filePath,
-                currentNamespace,
-                linkGenerator,
+        if (scanResult?.action === "match") {
+            const occurrence = scanResult.occurrence
+            const candidateData = occurrence.replacementCandidateData
+                ?? occurrence.candidateData
+            const { linkPath, alias } = resolveLinkContent(
+                candidateData,
+                occurrence.text,
                 settings,
+                resolvedAmbiguities,
             )
-            if (fallbackResult) {
-                result += fallbackResult.result
-                i = fallbackResult.newIndex
-                continue outer
-            }
+            const finalLink = linkGenerator({
+                linkPath,
+                sourcePath: filePath,
+                alias,
+                isInTable: forceIsInTable ?? occurrence.isInTable,
+            })
+            result += finalLink
+            i = occurrence.end
+            continue
         }
 
-        // If no rule applies, output the current character
         result += text[i]
         i++
     }
@@ -846,6 +291,7 @@ export const replaceLinks = ({
         ignoreDateFormats: true,
     },
     linkGenerator = defaultLinkGenerator,
+    resolvedAmbiguities,
 }: ReplaceLinksOptions): string => {
     // Normalize the body text to NFC
     body = body.normalize("NFC")
@@ -860,9 +306,45 @@ export const replaceLinks = ({
 
     // Get the current namespace
     const currentNamespace = getCurrentNamespace(filePath, settings.baseDir)
+    let bodyWithResolvedWikilinks = body
+
+    const markdownOptions = {
+        protectHeadings: settings.ignoreHeadings,
+        protectCallouts: true,
+        protectTableRows: settings.ignoreMarkdownTables,
+        protectUrls: true,
+    }
+
+    const replaceResolvedWikilink = (
+        wikilink: string,
+        start: number,
+    ): string => {
+        if (!resolvedAmbiguities?.has(wikilink)) {
+            return wikilink
+        }
+
+        const resolvedPath = resolvedAmbiguities.get(wikilink)!
+        const { linkPath, alias: resolvedAlias } = extractLinkParts(resolvedPath)
+        const existingLinkRegex = /\[\[([^|\]]+)(?:\|([^\]]+))?\]\]/
+        const linkMatch = wikilink.match(existingLinkRegex)
+        const existingPath = linkMatch ? linkMatch[1] : ""
+        const existingAlias = linkMatch ? linkMatch[2] : undefined
+        const finalAlias = resolvedAlias || existingAlias || (wikilink.includes("|") ? undefined : existingPath)
+
+        return linkGenerator({
+            linkPath,
+            sourcePath: filePath,
+            alias: finalAlias,
+            isInTable: !settings.ignoreMarkdownTables
+                && isIndexInsideMarkdownTable(body, start),
+        })
+    }
 
     // Process segments of text
-    const processTextSegment = (text: string): string => {
+    const processTextSegment = (
+        text: string,
+        forceIsInTable?: boolean,
+    ): string => {
         // Check if the text contains CJK characters
         const hasCjkText = isCjkText(text)
 
@@ -875,6 +357,8 @@ export const replaceLinks = ({
                 filePath,
                 linkGenerator,
                 settings,
+                resolvedAmbiguities,
+                forceIsInTable,
             )
         }
         else {
@@ -887,55 +371,61 @@ export const replaceLinks = ({
                 currentNamespace,
                 linkGenerator,
                 settings,
+                resolvedAmbiguities,
+                forceIsInTable,
             )
         }
     }
 
-    // Extract and protect callout blocks first
-    // Match callout blocks: starts with > [!type] and continues with lines starting with >
-    const calloutPattern = /^>[ \t]*\[![\w-]+\].*?(\n>.*?)*(?=\n(?!>)|$)/gm
-    const callouts: Array<{ placeholder: string, content: string }> = []
-    let calloutIndex = 0
-
-    // Replace callouts with placeholders
-    const bodyWithPlaceholders = body.replace(calloutPattern, (match) => {
-        const placeholder = `__CALLOUT_${calloutIndex}__`
-        callouts.push({ placeholder, content: match })
-        calloutIndex++
-        return placeholder
-    })
-
-    // Process the entire body while preserving protected segments
-    let resultBody = ""
-    let lastIndex = 0
-    let match: RegExpExecArray | null
-
-    // Reset the regex to start from the beginning
-    REGEX_PATTERNS.PROTECTED.lastIndex = 0
-
-    while (
-        (match = REGEX_PATTERNS.PROTECTED.exec(bodyWithPlaceholders)) !== null
-    ) {
-        const mIndex = match.index
-        const segment = bodyWithPlaceholders.slice(lastIndex, mIndex)
-        resultBody += processTextSegment(segment)
-        // Append the protected segment unchanged
-        resultBody += match[0]
-        lastIndex = mIndex + match[0].length
-
-        // Prevent infinite loop on zero-length matches
-        if (match[0].length === 0) {
-            REGEX_PATTERNS.PROTECTED.lastIndex++
+    const processTableAwareTextSegment = (
+        text: string,
+        segment: { start: number },
+    ): string => {
+        if (!text.includes("\n")) {
+            const isInTable = !settings.ignoreMarkdownTables
+                && isIndexInsideMarkdownTable(bodyWithResolvedWikilinks, segment.start)
+            return processTextSegment(text, isInTable)
         }
+
+        return text.replace(/[^\n]*(?:\n|$)/g, (line, offset) => {
+            if (line === "") {
+                return line
+            }
+
+            const lineContent = line.endsWith("\n")
+                ? line.slice(0, -1).replace(/\r$/, "")
+                : line
+
+            if (lineContent === "") {
+                return line
+            }
+
+            const absoluteIndex = segment.start + offset
+            const isInTable = !settings.ignoreMarkdownTables
+                && isIndexInsideMarkdownTable(bodyWithResolvedWikilinks, absoluteIndex)
+
+            return processTextSegment(line, isInTable)
+        })
     }
 
-    // Process the remaining text
-    resultBody += processTextSegment(bodyWithPlaceholders.slice(lastIndex))
+    if (resolvedAmbiguities) {
+        bodyWithResolvedWikilinks = segmentMarkdown(body, markdownOptions)
+            .map((segment) => {
+                if (
+                    segment.kind === "protected"
+                    && segment.protectedKind === "wikilink"
+                ) {
+                    return replaceResolvedWikilink(segment.text, segment.start)
+                }
 
-    // Restore callouts
-    for (const { placeholder, content } of callouts) {
-        resultBody = resultBody.replace(placeholder, content)
+                return segment.text
+            })
+            .join("")
     }
 
-    return resultBody
+    return mapMarkdownProse(
+        bodyWithResolvedWikilinks,
+        processTableAwareTextSegment,
+        markdownOptions,
+    )
 }

src/replace-url-with-title/__tests__/replace-url-with-title.test.ts

@@ -63,4 +63,30 @@ describe("replaceUrlWithTitle", () => {
             "Line 1: [Example Title](https://example.com)\nLine 2: [Another Title](https://another.com)",
         )
     })
+
+    it("should ignore URLs inside tilde fenced code blocks", () => {
+        const body = "~~~\nhttps://example.com\n~~~"
+        const result = replaceUrlWithTitle({
+            body,
+            urlTitleMap: new Map(
+                Object.entries({
+                    "https://example.com": "Example Title",
+                }),
+            ),
+        })
+        expect(result).toBe("~~~\nhttps://example.com\n~~~")
+    })
+
+    it("should not replace angle-bracket autolinks", () => {
+        const body = "<https://example.com>"
+        const result = replaceUrlWithTitle({
+            body,
+            urlTitleMap: new Map(
+                Object.entries({
+                    "https://example.com": "Example Title",
+                }),
+            ),
+        })
+        expect(result).toBe("<https://example.com>")
+    })
 })

src/replace-url-with-title/index.ts

@@ -1,3 +1,5 @@
+import { mapMarkdownProse } from "../markdown-segments"
+
 type Url = string
 type Title = string
 interface ReplaceUrlWithTitleOptions {
@@ -13,103 +15,77 @@ export const replaceUrlWithTitle = ({
         return body
     }
 
-    let resultBody = body
-
     // Sort URLs by length descending to replace longer URLs first
     // This helps prevent partial replacements (e.g., replacing 'example.com' before 'sub.example.com')
     const sortedUrls = Array.from(urlTitleMap.keys()).sort(
         (a, b) => b.length - a.length,
     )
 
-    for (const url of sortedUrls) {
-        const title = urlTitleMap.get(url)
-        // Should not happen with Map iteration, but good practice
-        if (!title) continue
+    const replaceUrlsInProse = (prose: string): string => {
+        let resultBody = prose
 
-        // Escape backslashes and special characters in title for link text safety if needed
-        // For now, assume title is safe.
-        const markdownLink = `[${title}](${url})`
-        let currentIndex = 0
-        const newBodyParts: string[] = []
+        for (const url of sortedUrls) {
+            const title = urlTitleMap.get(url)
+            if (!title) continue
 
-        // Find all occurrences of the current URL in the resultBody
-        // resultBody is updated in each iteration of the outer loop
-        while (currentIndex < resultBody.length) {
-            // Find the next occurrence of the URL, case-sensitive.
-            const nextOccurrence = resultBody.indexOf(url, currentIndex)
+            const markdownLink = `[${title}](${url})`
+            let currentIndex = 0
+            const newBodyParts: string[] = []
 
-            if (nextOccurrence === -1) {
-                // No more occurrences found, add the rest of the string
-                newBodyParts.push(resultBody.substring(currentIndex))
-                break
-            }
+            while (currentIndex < resultBody.length) {
+                const nextOccurrence = resultBody.indexOf(url, currentIndex)
 
-            // Add the text segment before the match
-            newBodyParts.push(
-                resultBody.substring(currentIndex, nextOccurrence),
-            )
+                if (nextOccurrence === -1) {
+                    newBodyParts.push(resultBody.substring(currentIndex))
+                    break
+                }
 
-            // --- Context Check ---
-            let shouldReplace = true
+                newBodyParts.push(
+                    resultBody.substring(currentIndex, nextOccurrence),
+                )
 
-            // 1. Check if already part of a Markdown link: [...](url)
-            // Look for `](` immediately before the URL and `)` immediately after.
-            const precedingChars = resultBody.substring(
-                nextOccurrence - 2,
-                nextOccurrence,
-            )
-            const followingChar = resultBody[nextOccurrence + url.length]
-            if (precedingChars === "](" && followingChar === ")") {
-                shouldReplace = false
-            }
+                let shouldReplace = true
 
-            // 2. Check if inside inline code: `... url ...`
-            // Count non-escaped backticks before the match. Odd count means inside code.
-            if (shouldReplace) {
-                const segmentBefore = resultBody.substring(0, nextOccurrence)
-                // Count non-escaped backticks `(?<!\\)` ensures we don't count escaped ones like \`
-                const backticksCount = (segmentBefore.match(/(?<!\\)`/g) || [])
-                    .length
+                const precedingChars = resultBody.substring(
+                    nextOccurrence - 2,
+                    nextOccurrence,
+                )
+                const precedingChar = resultBody[nextOccurrence - 1]
+                const followingChar = resultBody[nextOccurrence + url.length]
+                if (
+                    (precedingChars === "](" && followingChar === ")")
+                    || (precedingChar === "<" && followingChar === ">")
+                ) {
+                    shouldReplace = false
+                }
 
-                if (backticksCount % 2 !== 0) {
-                    // Odd number of backticks means we might be inside a code span.
-                    // We need to ensure the code span doesn't close before our match.
-                    const lastBacktickIndex = segmentBefore.lastIndexOf("`")
-                    // Check if there's another backtick between the last one and the match.
-                    // If not, we are inside the code span.
-                    if (
-                        lastBacktickIndex !== -1
-                        && !segmentBefore
-                            .substring(lastBacktickIndex + 1)
-                            .includes("`")
-                    ) {
-                        shouldReplace = false
+                if (shouldReplace) {
+                    const segmentBefore = resultBody.substring(0, nextOccurrence)
+                    const backticksCount = (segmentBefore.match(/(?<!\\)`/g) || [])
+                        .length
+
+                    if (backticksCount % 2 !== 0) {
+                        const lastBacktickIndex = segmentBefore.lastIndexOf("`")
+                        if (
+                            lastBacktickIndex !== -1
+                            && !segmentBefore
+                                .substring(lastBacktickIndex + 1)
+                                .includes("`")
+                        ) {
+                            shouldReplace = false
+                        }
                     }
                 }
+
+                newBodyParts.push(shouldReplace ? markdownLink : url)
+                currentIndex = nextOccurrence + url.length
             }
 
-            // 3. Check if inside fenced code block: ``` ... url ... ```
-            // This check is complex and not implemented here for simplicity.
-            // Assumes URLs within fenced code blocks should not be replaced by default.
-            // A simple heuristic could check the lines around the match for ```,
-            // but a proper parser state would be needed for accuracy.
-
-            // --- Apply Replacement ---
-            if (shouldReplace) {
-                newBodyParts.push(markdownLink)
-            }
-            else {
-                // Keep the original URL if context checks failed
-                newBodyParts.push(url)
-            }
-
-            // Move index past the current match (either the original url or the replaced markdownLink)
-            // Use url.length because that's what we searched for.
-            currentIndex = nextOccurrence + url.length
+            resultBody = newBodyParts.join("")
         }
-        // Update resultBody for the next URL in the outer loop
-        resultBody = newBodyParts.join("")
+
+        return resultBody
     }
 
-    return resultBody
+    return mapMarkdownProse(body, replaceUrlsInProse)
 }

src/replace-url-with-title/utils/__tests__/list-up-all-urls.test.ts

@@ -32,6 +32,12 @@ describe("listupAllUrls", () => {
         expect(result).not.toContain("https://example.com")
     })
 
+    it("should ignore URLs inside tilde fenced code blocks", () => {
+        const body = "~~~\nhttps://example.com\n~~~"
+        const result = listupAllUrls(body)
+        expect(result).not.toContain("https://example.com")
+    })
+
     it("ignore domains", () => {
         const body = "Check this link: https://example.com"
         const result = listupAllUrls(body, ["example.com"])

src/replace-url-with-title/utils/list-up-all-urls.ts

@@ -1,3 +1,5 @@
+import { segmentMarkdown } from "../../markdown-segments"
+
 type Url = string
 
 // Regular expression to find URLs starting with http:// or https://
@@ -16,159 +18,79 @@ export const listupAllUrls = (
     const urls = new Set<Url>()
     let match
 
-    // --- Pre-calculate Fenced Code Block Ranges ---
-    const codeBlockRanges: { start: number, end: number }[] = []
-    // Regex to find fenced code blocks (handles different fence lengths and optional language specifiers)
-    // Matches from ``` or ~~~ at the start of a line to the next ``` or ~~~ at the start of a line
-    const codeBlockRegex
-        = /^(?:```|~~~)[^\r\n]*?\r?\n([\s\S]*?)\r?\n^(?:```|~~~)$/gm
-    let blockMatch
-    while ((blockMatch = codeBlockRegex.exec(body)) !== null) {
-        codeBlockRanges.push({
-            start: blockMatch.index,
-            end: blockMatch.index + blockMatch[0].length,
-        })
-    }
-    // Reset regex state if needed, though new exec calls should handle this
-    codeBlockRegex.lastIndex = 0
+    for (const segment of segmentMarkdown(body)) {
+        if (segment.kind === "protected") {
+            continue
+        }
 
-    while ((match = URL_REGEX.exec(body)) !== null) {
-        const url = match[0]
-        const matchIndex = match.index
+        URL_REGEX.lastIndex = 0
+        while ((match = URL_REGEX.exec(segment.text)) !== null) {
+            const url = match[0]
+            const matchIndex = segment.start + match.index
 
-        // --- Fenced Code Block Check ---
-        // Check if the match index falls within any calculated code block range
-        let isInCodeBlock = false
-        for (const range of codeBlockRanges) {
-            if (matchIndex >= range.start && matchIndex < range.end) {
-                isInCodeBlock = true
-                break
+            let isBareUrl = true
+
+            if (matchIndex >= 2) {
+                const followingCharIndex = matchIndex + url.length
+                if (followingCharIndex < body.length && body[followingCharIndex] === ")") {
+                    const precedingChars = body.substring(matchIndex - 2, matchIndex)
+                    if (precedingChars === "](") {
+                        isBareUrl = false
+                    }
+                }
             }
-        }
-        if (isInCodeBlock) {
-            continue // Skip this URL if it's inside a fenced code block
-        }
 
-        // --- Context Check ---
-        let isBareUrl = true
-
-        // 1. Check if already part of a Markdown link: [...](url)
-        if (matchIndex >= 2) { // Need space for "]("
-            // Check if the URL is potentially followed by ')'
-            const followingCharIndex = matchIndex + url.length
-            if (followingCharIndex < body.length && body[followingCharIndex] === ")") {
-                // If followed by ')', check if preceded by "]("
-                const precedingChars = body.substring(matchIndex - 2, matchIndex)
-                if (precedingChars === "](") {
-                    // Only if both conditions are met, it's a Markdown link
+            if (isBareUrl && matchIndex >= 1) {
+                const precedingChar = body[matchIndex - 1]
+                const followingChar = body[matchIndex + url.length]
+                if (precedingChar === "<" && followingChar === ">") {
                     isBareUrl = false
                 }
             }
-        }
 
-        // 2. Check if enclosed in angle brackets: <url>
-        if (isBareUrl && matchIndex >= 1) {
-            const precedingChar = body[matchIndex - 1]
-            const followingChar = body[matchIndex + url.length]
-            if (precedingChar === "<" && followingChar === ">") {
-                isBareUrl = false
-            }
-        }
+            if (isBareUrl) {
+                let finalUrl = url
+                let shouldAdd = true
 
-        // 3. Check if inside inline code: `... url ...`
-        // Count non-escaped backticks before the match. Odd count means inside code.
-        if (isBareUrl) {
-            const segmentBefore = body.substring(0, matchIndex)
-            // Count non-escaped backticks `(?<!\\)` ensures we don't count escaped ones like \`
-            const backticksCount = (segmentBefore.match(/(?<!\\)`/g) || [])
-                .length
-
-            if (backticksCount % 2 !== 0) {
-                // Odd number of backticks means we might be inside a code span.
-                // We need to ensure the code span doesn't close *before* our match.
-                const lastBacktickIndex = segmentBefore.lastIndexOf("`")
-                // Check if there's another backtick between the last one and the match.
-                // If not, we are inside the code span.
-                if (
-                    lastBacktickIndex !== -1
-                    && !segmentBefore
-                        .substring(lastBacktickIndex + 1)
-                        .includes("`")
-                ) {
-                    isBareUrl = false
-                }
-            }
-        }
-
-        // 4. Check if inside fenced code block: ``` ... url ... ```
-        // This check remains complex. A simple heuristic: check if the line
-        // containing the URL is within a ``` block. This is not foolproof.
-        // For now, we'll skip this check for simplicity, but acknowledge it's a limitation.
-        // A more robust solution would involve parsing the Markdown structure.
-
-        // --- Check Ignored Domains & Clean URL ---
-        if (isBareUrl) {
-            let finalUrl = url
-            let shouldAdd = true
-
-            // 5. Check Ignored Domains
-            if (ignoredDomains && ignoredDomains.length > 0) {
-                try {
-                    const parsedUrl = new URL(url)
-                    const hostname = parsedUrl.hostname
-                    if (
-                        ignoredDomains.some(
-                            domain =>
-                                hostname === domain
-                                || hostname.endsWith(`.${domain}`),
+                if (ignoredDomains && ignoredDomains.length > 0) {
+                    try {
+                        const parsedUrl = new URL(url)
+                        const hostname = parsedUrl.hostname
+                        if (
+                            ignoredDomains.some(
+                                domain =>
+                                    hostname === domain
+                                    || hostname.endsWith(`.${domain}`),
+                            )
+                        ) {
+                            shouldAdd = false
+                        }
+                    }
+                    catch (e) {
+                        console.warn(
+                            `Failed to parse URL for domain check: ${url}`,
+                            e,
                         )
-                    ) {
                         shouldAdd = false
                     }
                 }
-                catch (e) {
-                    // If URL parsing fails, it's likely not a valid URL to add anyway
-                    console.warn(
-                        `Failed to parse URL for domain check: ${url}`,
-                        e,
-                    )
-                    shouldAdd = false
-                }
-            }
 
-            // 6. Clean Trailing Punctuation (only if not ignored)
-            // We only clean punctuation if the URL wasn't already excluded by context checks.
-            if (shouldAdd) {
-                const cleanedUrl = url.replace(TRAILING_PUNCTUATION_REGEX, "")
-                // Ensure cleaning didn't make it invalid (e.g., just "http://")
-                // or remove essential parts if the regex was too broad.
-                if (cleanedUrl.includes("://")) {
-                    finalUrl = cleanedUrl // Use the cleaned URL only if it's still valid-looking
+                if (shouldAdd) {
+                    const cleanedUrl = url.replace(TRAILING_PUNCTUATION_REGEX, "")
+                    if (cleanedUrl.includes("://")) {
+                        finalUrl = cleanedUrl
+                    }
+                    else {
+                        finalUrl = url
+                        console.warn(`URL cleaning potentially broke the URL: ${url} -> ${cleanedUrl}`)
+                    }
                 }
-                else {
-                    // If cleaning resulted in an invalid URL, maybe don't add it,
-                    // or reconsider the TRAILING_PUNCTUATION_REGEX.
-                    // For now, let's stick with the original URL if cleaning fails badly.
-                    // This case shouldn't happen often with the current regex.
-                    finalUrl = url // Revert to original if cleaning broke it
-                    console.warn(`URL cleaning potentially broke the URL: ${url} -> ${cleanedUrl}`)
-                    // Decide if we should still add the original potentially dirty url
-                    // shouldAdd = false; // Option: Don't add if cleaning failed
-                }
-            }
 
-            // --- Add URL if context checks pass and not ignored ---
-            if (shouldAdd) {
-                urls.add(finalUrl)
+                if (shouldAdd) {
+                    urls.add(finalUrl)
+                }
             }
         }
-
-        // Reset regex lastIndex to avoid issues with overlapping matches or zero-length matches
-        // Although our URL regex shouldn't produce zero-length matches.
-        // If the regex finds a match at index `i`, the next search starts at `i + 1`.
-        // If the match was length `l`, `exec` updates `lastIndex` to `i + l`.
-        // We need to ensure progress even if `l` is 0, but `URL_REGEX` won't match empty.
-        // If `isBareUrl` logic modified the string or indices, care would be needed.
     }
 
     return urls

src/replace-urls/__tests__/replace-urls.test.ts

@@ -4,6 +4,7 @@ import {
     DEFAULT_SETTINGS,
 } from "../../settings/settings-info"
 import { formatGitHubURL } from "../github"
+import { formatLinearURL } from "../linear"
 import { replaceURLs } from "../replace-urls"
 
 describe("replace-urls", () => {
@@ -13,12 +14,71 @@ describe("replace-urls", () => {
     }
 
     it("should replace GitHub URLs", () => {
-        const input
-            = "[[github/kdnk/obsidian-automatic-linker]] [🔗](https://github.com/kdnk/obsidian-automatic-linker)"
+        const input = "https://github.com/kdnk/obsidian-automatic-linker"
         const expected
             = "[[github/kdnk/obsidian-automatic-linker]] [🔗](https://github.com/kdnk/obsidian-automatic-linker)"
         expect(replaceURLs(input, baseSettings, formatGitHubURL)).toBe(
             expected,
         )
     })
+
+    it("does not rewrite https URLs inside wikilinks", () => {
+        const input = "[[https://github.com/kdnk/obsidian-automatic-linker]]"
+
+        expect(
+            replaceURLs(input, baseSettings, formatGitHubURL),
+        ).toBe(input)
+    })
+
+    it("should replace linear protocol URLs", () => {
+        const input = "linear://workspace/issue/ACME-123"
+        const expected
+            = "[[linear/workspace/ACME-123]] [🔗](https://linear.app/workspace/issue/ACME-123)"
+
+        expect(
+            replaceURLs(
+                input,
+                {
+                    ...baseSettings,
+                    formatLinearURLs: true,
+                },
+                formatLinearURL,
+            ),
+        ).toBe(expected)
+    })
+
+    it("does not rewrite linear protocol URLs inside wikilinks", () => {
+        const input = "[[linear://workspace/issue/ACME-123]]"
+
+        expect(
+            replaceURLs(
+                input,
+                {
+                    ...baseSettings,
+                    formatLinearURLs: true,
+                },
+                formatLinearURL,
+            ),
+        ).toBe(input)
+    })
+
+    it("keeps raw helper semantics inside Markdown links and angle autolinks", () => {
+        const input = [
+            "[label](https://github.com/kdnk/obsidian-automatic-linker)",
+            "<linear://workspace/issue/ACME-123>",
+        ].join(" ")
+
+        const expected = [
+            "[label](converted:https://github.com/kdnk/obsidian-automatic-linker)",
+            "<converted:linear://workspace/issue/ACME-123>",
+        ].join(" ")
+
+        expect(
+            replaceURLs(
+                input,
+                baseSettings,
+                url => `converted:${url}`,
+            ),
+        ).toBe(expected)
+    })
 })

src/replace-urls/__tests__/url-formatting.test.ts

@@ -0,0 +1,145 @@
+import { describe, expect, it } from "vitest"
+import { DEFAULT_SETTINGS } from "../../settings/settings-info"
+import {
+    formatURLsInText,
+    formatURLWithAdapters,
+    UrlFormatter,
+} from "../url-formatting"
+
+describe("formatURLWithAdapters", () => {
+    it("uses the first adapter that changes the URL", () => {
+        const first: UrlFormatter = url => `${url}-first`
+        const second: UrlFormatter = url => `${url}-second`
+
+        expect(
+            formatURLWithAdapters(
+                "https://example.com",
+                DEFAULT_SETTINGS,
+                [first, second],
+            ),
+        ).toBe("https://example.com-first")
+    })
+
+    it("returns the original URL when no adapter changes it", () => {
+        const unchanged: UrlFormatter = url => url
+
+        expect(
+            formatURLWithAdapters(
+                "https://example.com",
+                DEFAULT_SETTINGS,
+                [unchanged],
+            ),
+        ).toBe("https://example.com")
+    })
+})
+
+describe("formatURLsInText", () => {
+    it("formats GitHub, Jira, and Linear URLs in one text pass", () => {
+        const result = formatURLsInText({
+            text: [
+                "https://github.com/owner/repo/issues/123",
+                "https://jira.company.com/browse/ABC-456",
+                "https://linear.app/team/issue/BUG-789/title",
+                "linear://team/issue/BUG-790",
+            ].join("\n"),
+            settings: {
+                ...DEFAULT_SETTINGS,
+                githubEnterpriseURLs: [],
+                jiraURLs: ["jira.company.com"],
+                formatGitHubURLs: true,
+                formatJiraURLs: true,
+                formatLinearURLs: true,
+            },
+        })
+
+        expect(result).toBe([
+            "[[github/owner/repo/issues/123]] [🔗](https://github.com/owner/repo/issues/123)",
+            "[[company/jira/ABC/456]] [🔗](https://jira.company.com/browse/ABC-456)",
+            "[[linear/team/BUG-789]] [🔗](https://linear.app/team/issue/BUG-789)",
+            "[[linear/team/BUG-790]] [🔗](https://linear.app/team/issue/BUG-790)",
+        ].join("\n"))
+    })
+
+    it("does not format GitHub URLs wrapped in angle brackets", () => {
+        const result = formatURLsInText({
+            text: "<https://github.com/owner/repo/issues/123>",
+            settings: {
+                ...DEFAULT_SETTINGS,
+                formatGitHubURLs: true,
+            },
+        })
+
+        expect(result).toBe("<https://github.com/owner/repo/issues/123>")
+    })
+
+    it("leaves disabled adapter URLs unchanged", () => {
+        const result = formatURLsInText({
+            text: "https://linear.app/team/issue/BUG-789/title",
+            settings: {
+                ...DEFAULT_SETTINGS,
+                formatLinearURLs: false,
+            },
+        })
+
+        expect(result).toBe("https://linear.app/team/issue/BUG-789/title")
+    })
+
+    it("leaves Jira URLs with query strings unchanged", () => {
+        const result = formatURLsInText({
+            text: "https://jira.company.com/browse/ABC-456?focusedCommentId=12345",
+            settings: {
+                ...DEFAULT_SETTINGS,
+                jiraURLs: ["jira.company.com"],
+                formatJiraURLs: true,
+            },
+        })
+
+        expect(result).toBe(
+            "https://jira.company.com/browse/ABC-456?focusedCommentId=12345",
+        )
+    })
+
+    it("keeps closing parens and trailing punctuation outside formatted URLs", () => {
+        const result = formatURLsInText({
+            text: "See (https://github.com/owner/repo/issues/123).",
+            settings: {
+                ...DEFAULT_SETTINGS,
+                formatGitHubURLs: true,
+            },
+        })
+
+        expect(result).toBe(
+            "See ([[github/owner/repo/issues/123]] [🔗](https://github.com/owner/repo/issues/123)).",
+        )
+    })
+
+    it("does not format URLs inside protected Markdown segments", () => {
+        const result = formatURLsInText({
+            text: [
+                "`https://github.com/owner/repo/issues/123`",
+                "```md",
+                "https://github.com/owner/repo/issues/123",
+                "```",
+                "[label](https://github.com/owner/repo/issues/123)",
+                "[[https://github.com/owner/repo/issues/123]]",
+                "<https://github.com/owner/repo/issues/123>",
+                "https://github.com/owner/repo/issues/123",
+            ].join("\n"),
+            settings: {
+                ...DEFAULT_SETTINGS,
+                formatGitHubURLs: true,
+            },
+        })
+
+        expect(result).toBe([
+            "`https://github.com/owner/repo/issues/123`",
+            "```md",
+            "https://github.com/owner/repo/issues/123",
+            "```",
+            "[label](https://github.com/owner/repo/issues/123)",
+            "[[https://github.com/owner/repo/issues/123]]",
+            "<https://github.com/owner/repo/issues/123>",
+            "[[github/owner/repo/issues/123]] [🔗](https://github.com/owner/repo/issues/123)",
+        ].join("\n"))
+    })
+})

src/replace-urls/github.ts

@@ -1,6 +1,4 @@
 import { AutomaticLinkerSettings } from "../settings/settings-info"
-import { formatJiraURL } from "./jira"
-import { formatLinearURL } from "./linear"
 
 type GitHubURLInfo = {
     owner: string
@@ -36,7 +34,7 @@ export function formatGitHubURL(
         const cleanURL = getCleanURL(githubURL, urlInfo)
         return formatToObsidianLink(urlInfo, cleanURL)
     }
-    catch (_e) {
+    catch {
         // If URL is invalid, return original string
         return url
     }
@@ -124,31 +122,3 @@ function isPullRequestOrIssueURL(url: URL): boolean {
     const path = url.pathname.toLowerCase()
     return path.includes("/pull/") || path.includes("/issues/")
 }
-
-export function formatURL(
-    url: string,
-    settings: AutomaticLinkerSettings,
-): string {
-    if (settings.formatGitHubURLs) {
-        const formattedGitHubURL = formatGitHubURL(url, settings)
-        if (formattedGitHubURL !== url) {
-            return formattedGitHubURL
-        }
-    }
-
-    if (settings.formatJiraURLs) {
-        const formattedJiraURL = formatJiraURL(url, settings)
-        if (formattedJiraURL !== url) {
-            return formattedJiraURL
-        }
-    }
-
-    if (settings.formatLinearURLs) {
-        const formattedLinearURL = formatLinearURL(url, settings)
-        if (formattedLinearURL !== url) {
-            return formattedLinearURL
-        }
-    }
-
-    return url
-}

src/replace-urls/jira.ts

@@ -37,7 +37,7 @@ export function formatJiraURL(
         const cleanURL = getCleanURL(jiraURL, urlInfo)
         return formatToObsidianLink(jiraURL, urlInfo, cleanURL)
     }
-    catch (_e) {
+    catch {
         // If URL is invalid, return original string
         return url
     }

src/replace-urls/linear.ts

@@ -43,7 +43,7 @@ export function formatLinearURL(
         const cleanURL = getCleanURL(urlInfo)
         return formatToObsidianLink(urlInfo, cleanURL)
     }
-    catch (_e) {
+    catch {
         // If URL is invalid, return original string
         return url
     }

src/replace-urls/replace-urls.ts

@@ -1,13 +1,39 @@
 import { AutomaticLinkerSettings } from "../settings/settings-info"
 
+const URL_PATTERN = /(?:https?:\/\/|linear:\/\/)[^\s<>\]]+/g
+const WIKILINK_PATTERN = /\[\[[\s\S]*?\]\]/g
+
+const collectWikilinkRanges = (text: string): Array<{ start: number, end: number }> => {
+    const ranges: Array<{ start: number, end: number }> = []
+    let match: RegExpExecArray | null
+
+    while ((match = WIKILINK_PATTERN.exec(text)) !== null) {
+        ranges.push({
+            start: match.index,
+            end: match.index + match[0].length,
+        })
+    }
+
+    return ranges
+}
+
+const isInsideRange = (
+    index: number,
+    ranges: Array<{ start: number, end: number }>,
+): boolean => ranges.some(range => index >= range.start && index < range.end)
+
 export const replaceURLs = (
     fileContent: string,
     settings: AutomaticLinkerSettings,
     formatter: (url: string, settings: AutomaticLinkerSettings) => string,
 ) => {
-    const githubUrlPattern = /(?<!\[\[.*)(https?:\/\/[^\s\]]+)(?!.*\]\])/g
-    fileContent = fileContent.replace(githubUrlPattern, (match) => {
+    const wikilinkRanges = collectWikilinkRanges(fileContent)
+
+    return fileContent.replace(URL_PATTERN, (match, offset) => {
+        if (isInsideRange(offset, wikilinkRanges)) {
+            return match
+        }
+
         return formatter(match, settings)
     })
-    return fileContent
 }

src/replace-urls/url-formatting.ts

@@ -0,0 +1,114 @@
+import { mapMarkdownProse } from "../markdown-segments"
+import { AutomaticLinkerSettings } from "../settings/settings-info"
+import { formatGitHubURL } from "./github"
+import { formatJiraURL } from "./jira"
+import { formatLinearURL } from "./linear"
+
+export type UrlFormatter = (
+    url: string,
+    settings: AutomaticLinkerSettings,
+) => string
+
+export interface FormatURLsInTextOptions {
+    text: string
+    settings: AutomaticLinkerSettings
+    formatters?: readonly UrlFormatter[]
+}
+
+const URL_PATTERN = /(?:https?:\/\/|linear:\/\/)[^\s<>\]]+/g
+
+const formatGitHubURLIfEnabled: UrlFormatter = (url, settings) =>
+    settings.formatGitHubURLs ? formatGitHubURL(url, settings) : url
+
+const formatJiraURLIfEnabled: UrlFormatter = (url, settings) =>
+    settings.formatJiraURLs ? formatJiraURL(url, settings) : url
+
+const formatLinearURLIfEnabled: UrlFormatter = (url, settings) =>
+    settings.formatLinearURLs ? formatLinearURL(url, settings) : url
+
+const TRAILING_PUNCTUATION = new Set([".", ",", ";", "!", "?", "]", "}"])
+
+const countCharacter = (text: string, character: string): number => {
+    let count = 0
+
+    for (const currentCharacter of text) {
+        if (currentCharacter === character) {
+            count += 1
+        }
+    }
+
+    return count
+}
+
+const splitTrailingBoundary = (match: string): { url: string, suffix: string } => {
+    let url = match
+    let suffix = ""
+
+    while (url.length > 0) {
+        const lastCharacter = url[url.length - 1]
+
+        if (TRAILING_PUNCTUATION.has(lastCharacter)) {
+            suffix = lastCharacter + suffix
+            url = url.slice(0, -1)
+            continue
+        }
+
+        if (
+            lastCharacter === ")"
+            && countCharacter(url, "(") < countCharacter(url, ")")
+        ) {
+            suffix = lastCharacter + suffix
+            url = url.slice(0, -1)
+            continue
+        }
+
+        break
+    }
+
+    return { url, suffix }
+}
+
+export const DEFAULT_URL_FORMATTERS: readonly UrlFormatter[] = [
+    formatGitHubURLIfEnabled,
+    formatJiraURLIfEnabled,
+    formatLinearURLIfEnabled,
+]
+
+export const formatURLWithAdapters = (
+    url: string,
+    settings: AutomaticLinkerSettings,
+    formatters: readonly UrlFormatter[] = DEFAULT_URL_FORMATTERS,
+): string => {
+    for (const formatter of formatters) {
+        const formatted = formatter(url, settings)
+        if (formatted !== url) {
+            return formatted
+        }
+    }
+
+    return url
+}
+
+export const formatURLsInText = ({
+    text,
+    settings,
+    formatters = DEFAULT_URL_FORMATTERS,
+}: FormatURLsInTextOptions): string =>
+    mapMarkdownProse(
+        text,
+        (prose, segment) =>
+            prose.replace(URL_PATTERN, (match, offset) => {
+                const precedingCharacter = offset > 0
+                    ? segment.text[offset - 1]
+                    : undefined
+                const followingCharacter = segment.text[offset + match.length]
+
+                if (precedingCharacter === "<" && followingCharacter === ">") {
+                    return match
+                }
+
+                const { url, suffix } = splitTrailingBoundary(match)
+
+                return formatURLWithAdapters(url, settings, formatters) + suffix
+            }),
+    )

src/settings/__tests__/settings-catalog.test.ts

@@ -0,0 +1,167 @@
+import { describe, expect, it } from "vitest"
+import {
+    DEFAULT_SETTINGS,
+    SETTINGS_CATALOG,
+    projectReplaceLinksSettings,
+    projectUrlFormattingSettings,
+    settingRefreshesIndex,
+} from "../settings-catalog"
+
+describe("SETTINGS_CATALOG", () => {
+    it("covers every default setting exactly once", () => {
+        const defaultKeys = Object.keys(DEFAULT_SETTINGS).sort()
+        const catalogKeys = SETTINGS_CATALOG.map(entry => entry.key).sort()
+
+        expect(catalogKeys).toEqual(defaultKeys)
+        expect(new Set(catalogKeys).size).toBe(catalogKeys.length)
+    })
+
+    it("groups settings by user workflow in display order", () => {
+        const expectedGroups = [
+            {
+                group: "Formatting Workflow",
+                keys: [
+                    "formatOnSave",
+                    "formatDelayMs",
+                    "runPrettierAfterFormatting",
+                    "runLinterAfterFormatting",
+                ],
+            },
+            {
+                group: "Link Behavior",
+                keys: [
+                    "respectNewFileFolderPath",
+                    "proximityBasedLinking",
+                    "includeAliases",
+                    "removeAliasInDirs",
+                    "ignoreCase",
+                    "matchSentenceCase",
+                ],
+            },
+            {
+                group: "Exclusions",
+                keys: [
+                    "preventSelfLinking",
+                    "ignoreDateFormats",
+                    "ignoreHeadings",
+                    "ignoreMarkdownTables",
+                    "excludeDirsFromAutoLinking",
+                ],
+            },
+            {
+                group: "URL Formatting",
+                keys: [
+                    "formatGitHubURLs",
+                    "githubEnterpriseURLs",
+                    "formatJiraURLs",
+                    "jiraURLs",
+                    "formatLinearURLs",
+                    "replaceUrlWithTitle",
+                    "replaceUrlWithTitleIgnoreDomains",
+                ],
+            },
+            {
+                group: "AI Link Enhancement (Beta)",
+                keys: [
+                    "aiEnabled",
+                    "aiEndpoint",
+                    "aiModel",
+                    "aiMaxContext",
+                ],
+            },
+            {
+                group: "Diagnostics",
+                keys: ["showNotice", "debug"],
+            },
+        ]
+
+        const actualGroups = SETTINGS_CATALOG.reduce<Array<{
+            group: string
+            keys: Array<keyof typeof DEFAULT_SETTINGS>
+        }>>((groups, entry) => {
+            const currentGroup = groups[groups.length - 1]
+            if (currentGroup?.group === entry.group) {
+                currentGroup.keys.push(entry.key)
+                return groups
+            }
+
+            groups.push({
+                group: entry.group,
+                keys: [entry.key],
+            })
+            return groups
+        }, [])
+
+        expect(actualGroups).toEqual(expectedGroups)
+    })
+
+    it("marks only the URL textarea settings for explicit sizing", () => {
+        const sizedTextareaKeys = SETTINGS_CATALOG
+            .filter(entry => entry.control === "textarea")
+            .filter(entry => (entry as { rows?: number }).rows === 4)
+            .filter(entry => (entry as { cols?: number }).cols === 50)
+            .map(entry => entry.key)
+            .sort()
+
+        expect(sizedTextareaKeys).toEqual([
+            "githubEnterpriseURLs",
+            "jiraURLs",
+            "replaceUrlWithTitleIgnoreDomains",
+        ])
+    })
+
+    it("marks current index-refresh settings", () => {
+        expect(settingRefreshesIndex("respectNewFileFolderPath")).toBe(true)
+        expect(settingRefreshesIndex("includeAliases")).toBe(true)
+        expect(settingRefreshesIndex("proximityBasedLinking")).toBe(true)
+        expect(settingRefreshesIndex("ignoreDateFormats")).toBe(true)
+        expect(settingRefreshesIndex("ignoreCase")).toBe(true)
+        expect(settingRefreshesIndex("preventSelfLinking")).toBe(true)
+        expect(settingRefreshesIndex("excludeDirsFromAutoLinking")).toBe(true)
+        expect(settingRefreshesIndex("removeAliasInDirs")).toBe(true)
+        expect(settingRefreshesIndex("debug")).toBe(false)
+    })
+})
+
+describe("settings projections", () => {
+    it("projects link replacement settings", () => {
+        expect(projectReplaceLinksSettings({
+            ...DEFAULT_SETTINGS,
+            proximityBasedLinking: false,
+            ignoreDateFormats: false,
+            ignoreCase: false,
+            matchSentenceCase: false,
+            preventSelfLinking: true,
+            removeAliasInDirs: ["archive"],
+            ignoreHeadings: true,
+            ignoreMarkdownTables: true,
+        }, "pages")).toEqual({
+            proximityBasedLinking: false,
+            baseDir: "pages",
+            ignoreDateFormats: false,
+            ignoreCase: false,
+            matchSentenceCase: false,
+            preventSelfLinking: true,
+            removeAliasInDirs: ["archive"],
+            ignoreHeadings: true,
+            ignoreMarkdownTables: true,
+        })
+    })
+
+    it("projects URL formatting settings", () => {
+        expect(projectUrlFormattingSettings({
+            ...DEFAULT_SETTINGS,
+            formatGitHubURLs: false,
+            githubEnterpriseURLs: ["github.enterprise.com"],
+            formatJiraURLs: false,
+            jiraURLs: ["jira.example.com"],
+            formatLinearURLs: true,
+        })).toEqual({
+            formatGitHubURLs: false,
+            githubEnterpriseURLs: ["github.enterprise.com"],
+            formatJiraURLs: false,
+            jiraURLs: ["jira.example.com"],
+            formatLinearURLs: true,
+        })
+    })
+})

src/settings/settings-catalog.ts

@@ -0,0 +1,388 @@
+import { ReplaceLinksSettings } from "../replace-links/replace-links"
+
+export type AutomaticLinkerSettings = {
+    formatOnSave: boolean
+    showNotice: boolean
+    respectNewFileFolderPath: boolean
+    includeAliases: boolean
+    proximityBasedLinking: boolean
+    ignoreDateFormats: boolean
+    ignoreHeadings: boolean
+    formatGitHubURLs: boolean
+    githubEnterpriseURLs: string[]
+    formatJiraURLs: boolean
+    jiraURLs: string[]
+    formatLinearURLs: boolean
+    debug: boolean
+    ignoreCase: boolean
+    matchSentenceCase: boolean
+    replaceUrlWithTitle: boolean
+    replaceUrlWithTitleIgnoreDomains: string[]
+    excludeDirsFromAutoLinking: string[]
+    preventSelfLinking: boolean
+    removeAliasInDirs: string[]
+    ignoreMarkdownTables: boolean
+    runLinterAfterFormatting: boolean
+    runPrettierAfterFormatting: boolean
+    formatDelayMs: number
+    aiEnabled: boolean
+    aiEndpoint: string
+    aiModel: string
+    aiMaxContext: number
+}
+
+export type SettingControl = "toggle" | "text" | "textarea"
+
+export interface SettingCatalogEntry<K extends keyof AutomaticLinkerSettings = keyof AutomaticLinkerSettings> {
+    key: K
+    group: string
+    name: string
+    description: string
+    control: SettingControl
+    placeholder?: string
+    multiline?: boolean
+    rows?: number
+    cols?: number
+    refreshesIndex: boolean
+    runtimeOnly?: boolean
+}
+
+export const DEFAULT_SETTINGS: AutomaticLinkerSettings = {
+    formatOnSave: false,
+    showNotice: false,
+    respectNewFileFolderPath: true,
+    includeAliases: true,
+    proximityBasedLinking: true,
+    ignoreDateFormats: true,
+    ignoreHeadings: false,
+    formatGitHubURLs: true,
+    githubEnterpriseURLs: [],
+    formatJiraURLs: true,
+    jiraURLs: [],
+    formatLinearURLs: false,
+    debug: false,
+    ignoreCase: true,
+    matchSentenceCase: true,
+    replaceUrlWithTitle: true,
+    replaceUrlWithTitleIgnoreDomains: [],
+    excludeDirsFromAutoLinking: [],
+    preventSelfLinking: false,
+    removeAliasInDirs: [],
+    ignoreMarkdownTables: false,
+    runLinterAfterFormatting: false,
+    runPrettierAfterFormatting: false,
+    formatDelayMs: 1,
+    aiEnabled: false,
+    aiEndpoint: "http://localhost:1234/v1",
+    aiModel: "gemma-4-7b",
+    aiMaxContext: 500,
+}
+
+export const SETTINGS_CATALOG = [
+    {
+        key: "formatOnSave",
+        group: "Formatting Workflow",
+        name: "Format on save",
+        description:
+            "When enabled, the file will be automatically formatted (links replaced) when saving.",
+        control: "toggle",
+        refreshesIndex: false,
+    },
+    {
+        key: "formatDelayMs",
+        group: "Formatting Workflow",
+        name: "Format delay (ms)",
+        description:
+            "Delay in milliseconds before formatting. Increase this value if the linter/prettier runs before the file is fully saved.",
+        control: "text",
+        placeholder: "e.g. 100",
+        refreshesIndex: false,
+    },
+    {
+        key: "runPrettierAfterFormatting",
+        group: "Formatting Workflow",
+        name: "Run Prettier after formatting",
+        description:
+            "When enabled, Prettier will be executed after Automatic Linker formatting. This requires prettier-format plugin to be installed. https://github.com/dylanarmstrong/obsidian-prettier-plugin",
+        control: "toggle",
+        refreshesIndex: false,
+    },
+    {
+        key: "runLinterAfterFormatting",
+        group: "Formatting Workflow",
+        name: "Run Obsidian Linter after formatting",
+        description:
+            "When enabled, Obsidian Linter will be executed after Automatic Linker formatting. This requires the Obsidian Linter plugin to be installed.",
+        control: "toggle",
+        refreshesIndex: false,
+    },
+    {
+        key: "respectNewFileFolderPath",
+        group: "Link Behavior",
+        name: "Respect 'Folder to create new notes in' setting",
+        description:
+            "When enabled, the plugin will use Obsidian's 'Folder to create new notes in' setting as the base directory for omitting folder prefixes in links.",
+        control: "toggle",
+        refreshesIndex: true,
+    },
+    {
+        key: "proximityBasedLinking",
+        group: "Link Behavior",
+        name: "Proximity-based linking",
+        description:
+            "When enabled, the plugin will automatically resolve namespaces for shorthand links. If multiple candidates share the same shorthand, the candidate with the most common path segments relative to the current file will be selected.",
+        control: "toggle",
+        refreshesIndex: true,
+    },
+    {
+        key: "includeAliases",
+        group: "Link Behavior",
+        name: "Include aliases",
+        description:
+            "When enabled, aliases will be included when processing links. Note: A restart is required for changes to take effect.",
+        control: "toggle",
+        refreshesIndex: true,
+    },
+    {
+        key: "removeAliasInDirs",
+        group: "Link Behavior",
+        name: "Remove aliases in directories",
+        description:
+            "Directories where link aliases should be removed, one per line (e.g. 'dir' will convert [[dir/xxx|yyy]] to [[dir/xxx]]). This affects both auto-generated aliases and frontmatter aliases.",
+        control: "textarea",
+        placeholder: "dir1\ndir2/subdir",
+        multiline: true,
+        refreshesIndex: true,
+    },
+    {
+        key: "ignoreCase",
+        group: "Link Behavior",
+        name: "Ignore case",
+        description:
+            "When enabled, link matching will be case-insensitive. The original case of the text will be preserved in the link.",
+        control: "toggle",
+        refreshesIndex: true,
+    },
+    {
+        key: "matchSentenceCase",
+        group: "Link Behavior",
+        name: "Match sentence case",
+        description:
+            "When 'Ignore case' is OFF, match text that is capitalized at the start of a sentence. For example, 'My name' at a sentence start will match the file 'my name'. This setting is ignored when 'Ignore case' is ON.",
+        control: "toggle",
+        refreshesIndex: false,
+    },
+    {
+        key: "preventSelfLinking",
+        group: "Exclusions",
+        name: "Prevent self-linking",
+        description:
+            "When enabled, text will not be linked to its own file. For example, the word 'VPN' inside VPN.md will not be converted to a link.",
+        control: "toggle",
+        refreshesIndex: true,
+    },
+    {
+        key: "ignoreDateFormats",
+        group: "Exclusions",
+        name: "Ignore date formats",
+        description:
+            "When enabled, links that match date formats (e.g. 2025-02-10) will be ignored. This helps maintain compatibility with Obsidian Tasks.",
+        control: "toggle",
+        refreshesIndex: true,
+    },
+    {
+        key: "ignoreHeadings",
+        group: "Exclusions",
+        name: "Ignore headings",
+        description:
+            "When enabled, headings (lines starting with #) will not have links added to them.",
+        control: "toggle",
+        refreshesIndex: false,
+    },
+    {
+        key: "ignoreMarkdownTables",
+        group: "Exclusions",
+        name: "Ignore Markdown tables",
+        description:
+            "When enabled, Markdown table rows will not have links added to them.",
+        control: "toggle",
+        refreshesIndex: false,
+    },
+    {
+        key: "excludeDirsFromAutoLinking",
+        group: "Exclusions",
+        name: "Exclude directories from automatic linking",
+        description:
+            "Directories to be excluded from automatic linking, one per line (e.g. 'Templates')",
+        control: "textarea",
+        placeholder: "Templates\nArchive",
+        multiline: true,
+        refreshesIndex: true,
+    },
+    {
+        key: "formatGitHubURLs",
+        group: "URL Formatting",
+        name: "Format GitHub URLs on save",
+        description:
+            "When enabled, GitHub URLs will be formatted when saving the file.",
+        control: "toggle",
+        refreshesIndex: false,
+    },
+    {
+        key: "githubEnterpriseURLs",
+        group: "URL Formatting",
+        name: "GitHub Enterprise URLs",
+        description:
+            "Add your GitHub Enterprise URLs, one per line (e.g. github.enterprise.com)",
+        control: "textarea",
+        placeholder: "github.enterprise.com\ngithub.company.com",
+        multiline: true,
+        rows: 4,
+        cols: 50,
+        refreshesIndex: false,
+    },
+    {
+        key: "formatJiraURLs",
+        group: "URL Formatting",
+        name: "Format JIRA URLs on save",
+        description:
+            "When enabled, JIRA URLs will be formatted when saving the file.",
+        control: "toggle",
+        refreshesIndex: false,
+    },
+    {
+        key: "jiraURLs",
+        group: "URL Formatting",
+        name: "JIRA URLs",
+        description:
+            "Add your JIRA URLs, one per line (e.g. jira.enterprise.com)",
+        control: "textarea",
+        placeholder: "jira.enterprise.com\njira.company.com",
+        multiline: true,
+        rows: 4,
+        cols: 50,
+        refreshesIndex: false,
+    },
+    {
+        key: "formatLinearURLs",
+        group: "URL Formatting",
+        name: "Format Linear URLs on save",
+        description:
+            "When enabled, Linear URLs will be formatted when saving the file.",
+        control: "toggle",
+        refreshesIndex: false,
+    },
+    {
+        key: "replaceUrlWithTitle",
+        group: "URL Formatting",
+        name: "Replace URL with title",
+        description:
+            "When enabled, raw URLs will be replaced with [Page Title](URL). Requires fetching the URL content.",
+        control: "toggle",
+        refreshesIndex: false,
+    },
+    {
+        key: "replaceUrlWithTitleIgnoreDomains",
+        group: "URL Formatting",
+        name: "Ignore domains",
+        description:
+            "Ignore domains for replacing URLs with titles, one per line (e.g. x.com)",
+        control: "textarea",
+        placeholder: "",
+        multiline: true,
+        rows: 4,
+        cols: 50,
+        refreshesIndex: false,
+    },
+    {
+        key: "aiEnabled",
+        group: "AI Link Enhancement (Beta)",
+        name: "Enable AI Link Enhancement",
+        description:
+            "When enabled, an AI-powered link enhancer command will be available. It uses a local LLM to resolve ambiguous links and correct existing ones.",
+        control: "toggle",
+        refreshesIndex: false,
+    },
+    {
+        key: "aiEndpoint",
+        group: "AI Link Enhancement (Beta)",
+        name: "AI API Endpoint",
+        description:
+            "The URL of your OpenAI-compatible AI server (e.g. LM Studio, Ollama).",
+        control: "text",
+        placeholder: "http://localhost:1234/v1",
+        refreshesIndex: false,
+    },
+    {
+        key: "aiModel",
+        group: "AI Link Enhancement (Beta)",
+        name: "AI Model",
+        description: "The name of the model to use (e.g. gemma-4-7b).",
+        control: "text",
+        placeholder: "gemma-4-7b",
+        refreshesIndex: false,
+    },
+    {
+        key: "aiMaxContext",
+        group: "AI Link Enhancement (Beta)",
+        name: "Max Context Length",
+        description:
+            "Number of characters around the link to provide as context to the AI.",
+        control: "text",
+        placeholder: "500",
+        refreshesIndex: false,
+    },
+    {
+        key: "showNotice",
+        group: "Diagnostics",
+        name: "Show load notice",
+        description: "Display a notice when markdown files are loaded.",
+        control: "toggle",
+        refreshesIndex: false,
+    },
+    {
+        key: "debug",
+        group: "Diagnostics",
+        name: "Debug mode",
+        description:
+            "When enabled, debug information will be logged to the console.",
+        control: "toggle",
+        refreshesIndex: false,
+    },
+] as const satisfies readonly SettingCatalogEntry[]
+
+export const settingRefreshesIndex = (
+    key: keyof AutomaticLinkerSettings,
+): boolean => SETTINGS_CATALOG.find(entry => entry.key === key)?.refreshesIndex ?? false
+
+export const projectReplaceLinksSettings = (
+    settings: AutomaticLinkerSettings,
+    baseDir?: string,
+): ReplaceLinksSettings => ({
+    proximityBasedLinking: settings.proximityBasedLinking,
+    baseDir,
+    ignoreDateFormats: settings.ignoreDateFormats,
+    ignoreCase: settings.ignoreCase,
+    matchSentenceCase: settings.matchSentenceCase,
+    preventSelfLinking: settings.preventSelfLinking,
+    removeAliasInDirs: settings.removeAliasInDirs,
+    ignoreHeadings: settings.ignoreHeadings,
+    ignoreMarkdownTables: settings.ignoreMarkdownTables,
+})
+
+export const projectUrlFormattingSettings = (
+    settings: AutomaticLinkerSettings,
+): Pick<
+    AutomaticLinkerSettings,
+    | "formatGitHubURLs"
+    | "githubEnterpriseURLs"
+    | "formatJiraURLs"
+    | "jiraURLs"
+    | "formatLinearURLs"
+> => ({
+    formatGitHubURLs: settings.formatGitHubURLs,
+    githubEnterpriseURLs: settings.githubEnterpriseURLs,
+    formatJiraURLs: settings.formatJiraURLs,
+    jiraURLs: settings.jiraURLs,
+    formatLinearURLs: settings.formatLinearURLs,
+})

src/settings/settings-info.ts

@@ -1,47 +1,2 @@
-export type AutomaticLinkerSettings = {
-    formatOnSave: boolean
-    showNotice: boolean
-    respectNewFileFolderPath: boolean // Respect Obsidian's "Folder to create new notes in" setting as base directory
-    considerAliases: boolean // Consider aliases when linking
-    proximityBasedLinking: boolean // Automatically resolve namespaces for shorthand links
-    ignoreDateFormats: boolean // Ignore date formatted links (e.g. 2025-02-10)
-    formatGitHubURLs: boolean // Format GitHub URLs on save
-    githubEnterpriseURLs: string[] // List of GitHub Enterprise URLs
-    formatJiraURLs: boolean // Format Jira URLs on save
-    jiraURLs: string[] // List of Jira URLs (domains)
-    formatLinearURLs: boolean // Format Linear URLs on save
-    debug: boolean // Enable debug logging
-    ignoreCase: boolean // Ignore case when matching links
-    replaceUrlWithTitle: boolean // Replace raw URLs with [Title](URL)
-    replaceUrlWithTitleIgnoreDomains: string[] // List of domains to ignore when replacing URLs with titles
-    excludeDirsFromAutoLinking: string[] // Optional: List of directories to exclude from auto-linking
-    preventSelfLinking: boolean // Prevent linking text to its own file
-    removeAliasInDirs: string[] // Remove aliases for links in specified directories
-    runLinterAfterFormatting: boolean // Run Obsidian Linter after automatic linker formatting
-    runPrettierAfterFormatting: boolean // Run Prettier after automatic linker formatting
-    formatDelayMs: number // Delay in milliseconds before running linter after formatting
-}
-
-export const DEFAULT_SETTINGS: AutomaticLinkerSettings = {
-    formatOnSave: false,
-    showNotice: false,
-    respectNewFileFolderPath: false, // Default: do not respect Obsidian's "Folder to create new notes in" setting
-    considerAliases: true, // Default: consider aliases
-    proximityBasedLinking: true, // Default: enable automatic namespace resolution
-    ignoreDateFormats: true, // Default: ignore date formats (e.g. 2025-02-10)
-    formatGitHubURLs: true, // Default: format GitHub URLs
-    githubEnterpriseURLs: [], // Default: empty list
-    formatJiraURLs: true, // Default: format Jira URLs
-    jiraURLs: [], // Default: empty list
-    formatLinearURLs: false, // Default: format Linear URLs
-    debug: false, // Default: disable debug logging
-    ignoreCase: true, // Default: case-sensitive matching
-    replaceUrlWithTitle: true, // Default: enable replacing URLs with titles
-    replaceUrlWithTitleIgnoreDomains: [],
-    excludeDirsFromAutoLinking: [], // Default: no excluded directories
-    preventSelfLinking: false, // Default: allow self-linking (backward compatibility)
-    removeAliasInDirs: [], // Default: no directories for alias removal
-    runLinterAfterFormatting: false, // Default: do not run linter after formatting
-    runPrettierAfterFormatting: false, // Run Prettier after automatic linker formatting
-    formatDelayMs: 1, // Default: 1ms delay before running linter
-}
+export type { AutomaticLinkerSettings } from "./settings-catalog"
+export { DEFAULT_SETTINGS } from "./settings-catalog"

src/settings/settings.ts

@@ -1,5 +1,11 @@
 import { App, PluginSettingTab, Setting } from "obsidian"
 import AutomaticLinkerPlugin from "../main"
+import {
+    AutomaticLinkerSettings,
+    SETTINGS_CATALOG,
+    SettingCatalogEntry,
+    settingRefreshesIndex,
+} from "./settings-catalog"
 
 export class AutomaticLinkerPluginSettingsTab extends PluginSettingTab {
     plugin: AutomaticLinkerPlugin
@@ -8,388 +14,111 @@ export class AutomaticLinkerPluginSettingsTab extends PluginSettingTab {
         this.plugin = plugin
     }
 
+    private async setSettingValue<K extends keyof AutomaticLinkerSettings>(
+        key: K,
+        value: AutomaticLinkerSettings[K],
+    ) {
+        this.plugin.settings[key] = value
+        await this.plugin.saveData(this.plugin.settings)
+        if (key === "replaceUrlWithTitleIgnoreDomains") {
+            await this.plugin.buildUrlTitleMap()
+        }
+        if (settingRefreshesIndex(key)) {
+            this.plugin.refreshFileDataAndTrie()
+        }
+    }
+
+    private parseTextValue<K extends keyof AutomaticLinkerSettings>(
+        key: K,
+        currentValue: AutomaticLinkerSettings[K],
+        nextValue: string,
+    ): AutomaticLinkerSettings[K] | null {
+        if (typeof currentValue !== "number") {
+            return nextValue as AutomaticLinkerSettings[K]
+        }
+
+        const parsedValue = parseInt(nextValue)
+        if (isNaN(parsedValue)) {
+            return null
+        }
+        if (key === "formatDelayMs" && parsedValue < 0) {
+            return null
+        }
+        if (key === "aiMaxContext" && parsedValue <= 0) {
+            return null
+        }
+
+        return parsedValue as AutomaticLinkerSettings[K]
+    }
+
+    private renderSetting(containerEl: HTMLElement, entry: SettingCatalogEntry) {
+        const setting = new Setting(containerEl)
+            .setName(entry.name)
+            .setDesc(entry.description)
+        const value = this.plugin.settings[entry.key]
+
+        if (entry.control === "toggle") {
+            setting.addToggle((toggle) => {
+                toggle
+                    .setValue(Boolean(value))
+                    .onChange(async (nextValue) => {
+                        await this.setSettingValue(entry.key, nextValue as never)
+                    })
+            })
+            return
+        }
+
+        if (entry.control === "text") {
+            setting.addText((text) => {
+                text.setPlaceholder(entry.placeholder ?? "")
+                    .setValue(String(value))
+                    .onChange(async (nextValue) => {
+                        const parsedValue = this.parseTextValue(
+                            entry.key,
+                            value,
+                            nextValue,
+                        )
+                        if (parsedValue === null) {
+                            return
+                        }
+                        await this.setSettingValue(entry.key, parsedValue)
+                    })
+            })
+            return
+        }
+
+        setting.addTextArea((text) => {
+            text.setPlaceholder(entry.placeholder ?? "")
+                .setValue(Array.isArray(value) ? value.join("\n") : String(value))
+                .onChange(async (nextValue) => {
+                    await this.setSettingValue(
+                        entry.key,
+                        nextValue
+                            .split("\n")
+                            .map(item => item.trim())
+                            .filter(Boolean) as never,
+                    )
+                })
+            if (entry.rows !== undefined) {
+                text.inputEl.rows = entry.rows
+            }
+            if (entry.cols !== undefined) {
+                text.inputEl.cols = entry.cols
+            }
+        })
+    }
+
     display(): void {
         const { containerEl } = this
         containerEl.empty()
 
-        new Setting(containerEl).setName("General").setHeading()
-
-        // Toggle for "Format on Save" setting.
-        new Setting(containerEl)
-            .setName("Format on save")
-            .setDesc(
-                "When enabled, the file will be automatically formatted (links replaced) when saving.",
-            )
-            .addToggle((toggle) => {
-                toggle
-                    .setValue(this.plugin.settings.formatOnSave)
-                    .onChange(async (value) => {
-                        this.plugin.settings.formatOnSave = value
-                        await this.plugin.saveData(this.plugin.settings)
-                    })
-            })
-
-        // Toggle for respecting Obsidian's "Folder to create new notes in" setting
-        new Setting(containerEl)
-            .setName("Respect 'Folder to create new notes in' setting")
-            .setDesc(
-                "When enabled, the plugin will use Obsidian's 'Folder to create new notes in' setting as the base directory for omitting folder prefixes in links.",
-            )
-            .addToggle((toggle) => {
-                toggle
-                    .setValue(this.plugin.settings.respectNewFileFolderPath)
-                    .onChange(async (value) => {
-                        this.plugin.settings.respectNewFileFolderPath = value
-                        await this.plugin.saveData(this.plugin.settings)
-                    })
-            })
-
-        // Toggle for running linter after formatting
-        new Setting(containerEl)
-            .setName("Run Obsidian Linter after formatting")
-            .setDesc(
-                "When enabled, Obsidian Linter will be executed after Automatic Linker formatting. This requires the Obsidian Linter plugin to be installed.",
-            )
-            .addToggle((toggle) => {
-                toggle
-                    .setValue(this.plugin.settings.runLinterAfterFormatting)
-                    .onChange(async (value) => {
-                        this.plugin.settings.runLinterAfterFormatting = value
-                        await this.plugin.saveData(this.plugin.settings)
-                    })
-            })
-
-        // Toggle for running prettier after formatting
-        new Setting(containerEl)
-            .setName("Run Prettier after formatting")
-            .setDesc(
-                "When enabled, Prettier will be executed after Automatic Linker formatting. This requires prettier-format plugin to be installed. https://github.com/dylanarmstrong/obsidian-prettier-plugin",
-            )
-            .addToggle((toggle) => {
-                toggle
-                    .setValue(this.plugin.settings.runPrettierAfterFormatting)
-                    .onChange(async (value) => {
-                        this.plugin.settings.runPrettierAfterFormatting = value
-                        await this.plugin.saveData(this.plugin.settings)
-                    })
-            })
-
-        // Setting for linter delay
-        new Setting(containerEl)
-            .setName("Format delay (ms)")
-            .setDesc(
-                "Delay in milliseconds before formatting. Increase this value if the linter/prettier runs before the file is fully saved.",
-            )
-            .addText((text) => {
-                text.setPlaceholder("e.g. 100")
-                    .setValue(this.plugin.settings.formatDelayMs.toString())
-                    .onChange(async (value) => {
-                        const parsedValue = parseInt(value)
-                        if (!isNaN(parsedValue) && parsedValue >= 0) {
-                            this.plugin.settings.formatDelayMs = parsedValue
-                            await this.plugin.saveData(this.plugin.settings)
-                        }
-                    })
-            })
-
-        // Toggle for considering aliases.
-        new Setting(containerEl)
-            .setName("Consider aliases")
-            .setDesc(
-                "When enabled, aliases will be taken into account when processing links. Note: A restart is required for changes to take effect.",
-            )
-            .addToggle((toggle) => {
-                toggle
-                    .setValue(this.plugin.settings.considerAliases)
-                    .onChange(async (value) => {
-                        this.plugin.settings.considerAliases = value
-                        await this.plugin.saveData(this.plugin.settings)
-                    })
-            })
-
-        // Toggle for proximity-based linking.
-        new Setting(containerEl)
-            .setName("Proximity-based linking")
-            .setDesc(
-                "When enabled, the plugin will automatically resolve namespaces for shorthand links. If multiple candidates share the same shorthand, the candidate with the most common path segments relative to the current file will be selected.",
-            )
-            .addToggle((toggle) => {
-                toggle
-                    .setValue(this.plugin.settings.proximityBasedLinking)
-                    .onChange(async (value) => {
-                        this.plugin.settings.proximityBasedLinking = value
-                        await this.plugin.saveData(this.plugin.settings)
-                    })
-            })
-
-        // Toggle for ignoring date formats.
-        new Setting(containerEl)
-            .setName("Ignore date formats")
-            .setDesc(
-                "When enabled, links that match date formats (e.g. 2025-02-10) will be ignored. This helps maintain compatibility with Obsidian Tasks.",
-            )
-            .addToggle((toggle) => {
-                toggle
-                    .setValue(this.plugin.settings.ignoreDateFormats)
-                    .onChange(async (value) => {
-                        this.plugin.settings.ignoreDateFormats = value
-                        await this.plugin.saveData(this.plugin.settings)
-                    })
-            })
-
-        // Toggle for ignoring case in link matching
-        new Setting(containerEl)
-            .setName("Ignore case")
-            .setDesc(
-                "When enabled, link matching will be case-insensitive. The original case of the text will be preserved in the link.",
-            )
-            .addToggle((toggle) => {
-                toggle
-                    .setValue(this.plugin.settings.ignoreCase)
-                    .onChange(async (value) => {
-                        this.plugin.settings.ignoreCase = value
-                        await this.plugin.saveData(this.plugin.settings)
-                    })
-            })
-
-        // Toggle for preventing self-linking
-        new Setting(containerEl)
-            .setName("Prevent self-linking")
-            .setDesc(
-                "When enabled, text will not be linked to its own file. For example, the word 'VPN' inside VPN.md will not be converted to a link.",
-            )
-            .addToggle((toggle) => {
-                toggle
-                    .setValue(this.plugin.settings.preventSelfLinking)
-                    .onChange(async (value) => {
-                        this.plugin.settings.preventSelfLinking = value
-                        await this.plugin.saveData(this.plugin.settings)
-                    })
-            })
-
-        // Add excluding dirs that you wish to exclude from the automatic linking
-        new Setting(containerEl)
-            .setName("Exclude directories from automatic linking")
-            .setDesc(
-                "Directories to be excluded from automatic linking, one per line (e.g. 'Templates')",
-            )
-            .addTextArea((text) => {
-                text.setPlaceholder("Templates\nArchive")
-                    .setValue(
-                        this.plugin.settings.excludeDirsFromAutoLinking.join(
-                            "\n",
-                        ),
-                    )
-                    .onChange(async (value) => {
-                        // Split by newlines and filter out empty lines
-                        const dirs = value
-                            .split("\n")
-                            .map(dir => dir.trim())
-                            .filter(Boolean)
-                        this.plugin.settings.excludeDirsFromAutoLinking = dirs
-                        await this.plugin.saveData(this.plugin.settings)
-                    })
-            })
-
-        // Remove aliases for links in specified directories
-        new Setting(containerEl)
-            .setName("Remove aliases in directories")
-            .setDesc(
-                "Directories where link aliases should be removed, one per line (e.g. 'dir' will convert [[dir/xxx|yyy]] to [[dir/xxx]]). This affects both auto-generated aliases and frontmatter aliases.",
-            )
-            .addTextArea((text) => {
-                text.setPlaceholder("dir1\ndir2/subdir")
-                    .setValue(this.plugin.settings.removeAliasInDirs.join("\n"))
-                    .onChange(async (value) => {
-                        // Split by newlines and filter out empty lines
-                        const dirs = value
-                            .split("\n")
-                            .map(dir => dir.trim())
-                            .filter(Boolean)
-                        this.plugin.settings.removeAliasInDirs = dirs
-                        await this.plugin.saveData(this.plugin.settings)
-                    })
-            })
-
-        new Setting(containerEl)
-            .setName("URL Replacement with Title")
-            .setHeading()
-
-        // Toggle for replacing URLs with titles
-        new Setting(containerEl)
-            .setName("Replace URL with title")
-            .setDesc(
-                "When enabled, raw URLs will be replaced with [Page Title](URL). Requires fetching the URL content.",
-            )
-            .addToggle((toggle) => {
-                toggle
-                    .setValue(this.plugin.settings.replaceUrlWithTitle)
-                    .onChange(async (value) => {
-                        this.plugin.settings.replaceUrlWithTitle = value
-                        await this.plugin.saveData(this.plugin.settings)
-                    })
-            })
-
-        new Setting(containerEl)
-            .setName("Igonre domains")
-            .setDesc(
-                "Ignore domains for replacing URLs with titles, one per line (e.g. x.com)",
-            )
-            .addTextArea((text) => {
-                text.setPlaceholder("")
-                    .setValue(
-                        this.plugin.settings.replaceUrlWithTitleIgnoreDomains.join(
-                            "\n",
-                        ),
-                    )
-                    .onChange(async (value) => {
-                        // Split by newlines and filter out empty lines
-                        const urls = value
-                            .split("\n")
-                            .map(url => url.trim())
-                            .filter(Boolean)
-                        this.plugin.settings.replaceUrlWithTitleIgnoreDomains
-                            = urls
-                        await this.plugin.saveData(this.plugin.settings)
-                    })
-                // Make the text area taller
-                text.inputEl.rows = 4
-                text.inputEl.cols = 50
-            })
-
-        new Setting(containerEl)
-            .setName("URL Formatting for GitHub")
-            .setHeading()
-
-        // Toggle for formatting GitHub URLs on save
-        new Setting(containerEl)
-            .setName("Format GitHub URLs on save")
-            .setDesc(
-                "When enabled, GitHub URLs will be formatted when saving the file.",
-            )
-            .addToggle((toggle) => {
-                toggle
-                    .setValue(this.plugin.settings.formatGitHubURLs)
-                    .onChange(async (value) => {
-                        this.plugin.settings.formatGitHubURLs = value
-                        await this.plugin.saveData(this.plugin.settings)
-                    })
-            })
-
-        // Add GitHub Enterprise URLs setting
-        new Setting(containerEl)
-            .setName("GitHub Enterprise URLs")
-            .setDesc(
-                "Add your GitHub Enterprise URLs, one per line (e.g. github.enterprise.com)",
-            )
-            .addTextArea((text) => {
-                text.setPlaceholder("github.enterprise.com\ngithub.company.com")
-                    .setValue(
-                        this.plugin.settings.githubEnterpriseURLs.join("\n"),
-                    )
-                    .onChange(async (value) => {
-                        // Split by newlines and filter out empty lines
-                        const urls = value
-                            .split("\n")
-                            .map(url => url.trim())
-                            .filter(Boolean)
-                        this.plugin.settings.githubEnterpriseURLs = urls
-                        await this.plugin.saveData(this.plugin.settings)
-                    })
-                // Make the text area taller
-                text.inputEl.rows = 4
-                text.inputEl.cols = 50
-            })
-
-        new Setting(containerEl)
-            .setName("URL Formatting for Jira")
-            .setHeading()
-
-        // Toggle for formatting JIRA URLs on save
-        new Setting(containerEl)
-            .setName("Format JIRA URLs on save")
-            .setDesc(
-                "When enabled, JIRA URLs will be formatted when saving the file.",
-            )
-            .addToggle((toggle) => {
-                toggle
-                    .setValue(this.plugin.settings.formatJiraURLs)
-                    .onChange(async (value) => {
-                        this.plugin.settings.formatJiraURLs = value
-                        await this.plugin.saveData(this.plugin.settings)
-                    })
-            })
-
-        // Add JIRA URLs setting
-        new Setting(containerEl)
-            .setName("JIRA URLs")
-            .setDesc(
-                "Add your JIRA URLs, one per line (e.g. jira.enterprise.com)",
-            )
-            .addTextArea((text) => {
-                text.setPlaceholder("jira.enterprise.com\njira.company.com")
-                    .setValue(this.plugin.settings.jiraURLs.join("\n"))
-                    .onChange(async (value) => {
-                        // Split by newlines and filter out empty lines
-                        const urls = value
-                            .split("\n")
-                            .map(url => url.trim())
-                            .filter(Boolean)
-                        this.plugin.settings.jiraURLs = urls
-                        await this.plugin.saveData(this.plugin.settings)
-                    })
-                // Make the text area taller
-                text.inputEl.rows = 4
-                text.inputEl.cols = 50
-            })
-
-        new Setting(containerEl)
-            .setName("URL Formatting for Linear")
-            .setHeading()
-
-        // Toggle for formatting Linear URLs on save
-        new Setting(containerEl)
-            .setName("Format Linear URLs on save")
-            .setDesc(
-                "When enabled, Linear URLs will be formatted when saving the file.",
-            )
-            .addToggle((toggle) => {
-                toggle
-                    .setValue(this.plugin.settings.formatLinearURLs)
-                    .onChange(async (value) => {
-                        this.plugin.settings.formatLinearURLs = value
-                        await this.plugin.saveData(this.plugin.settings)
-                    })
-            })
-
-        new Setting(containerEl).setName("Debug").setHeading()
-
-        // Toggle for showing the load notice.
-        new Setting(containerEl)
-            .setName("Show load notice")
-            .setDesc("Display a notice when markdown files are loaded.")
-            .addToggle((toggle) => {
-                toggle
-                    .setValue(this.plugin.settings.showNotice)
-                    .onChange(async (value) => {
-                        this.plugin.settings.showNotice = value
-                        await this.plugin.saveData(this.plugin.settings)
-                    })
-            })
-
-        // Toggle for debug logging
-        new Setting(containerEl)
-            .setName("Debug mode")
-            .setDesc(
-                "When enabled, debug information will be logged to the console.",
-            )
-            .addToggle((toggle) => {
-                toggle
-                    .setValue(this.plugin.settings.debug)
-                    .onChange(async (value) => {
-                        this.plugin.settings.debug = value
-                        await this.plugin.saveData(this.plugin.settings)
-                    })
-            })
+        const renderedGroups = new Set<string>()
+        for (const entry of SETTINGS_CATALOG) {
+            if (!renderedGroups.has(entry.group)) {
+                new Setting(containerEl).setName(entry.group).setHeading()
+                renderedGroups.add(entry.group)
+            }
+            this.renderSetting(containerEl, entry)
+        }
     }
 }

src/trie.ts

@@ -63,12 +63,16 @@ export const buildTrie = (words: string[], ignoreCase = false): TrieNode => {
 }
 
 // CandidateData holds the canonical replacement string as well as namespace‐設定
-export interface CandidateData {
+export interface CandidateItem {
     canonical: string
     scoped: boolean
     namespace: string
 }
 
+export interface CandidateData {
+    candidates: CandidateItem[]
+}
+
 export const buildCandidateTrie = (
     allFiles: PathAndAliases[],
     baseDir: string | undefined,
@@ -104,10 +108,23 @@ export const buildCandidateTrie = (
     // Build a mapping from candidate string to its CandidateData.
     const candidateMap = new Map<string, CandidateData>()
 
+    const addCandidate = (key: string, item: CandidateItem) => {
+        const existing = candidateMap.get(key)
+        if (existing) {
+            // Check if this canonical path is already added to avoid duplicates
+            if (!existing.candidates.some(c => c.canonical === item.canonical)) {
+                existing.candidates.push(item)
+            }
+        }
+        else {
+            candidateMap.set(key, { candidates: [item] })
+        }
+    }
+
     // Register normal candidates.
     for (const { full, short, scoped, namespace } of candidates) {
-        // Register the full path and its case-insensitive variant if needed
-        candidateMap.set(full, {
+        // Register the full path
+        addCandidate(full, {
             canonical: full,
             scoped,
             namespace,
@@ -124,25 +141,21 @@ export const buildCandidateTrie = (
                     lastSegment,
                 )
             ) {
-                // Register both the original case and lowercase versions
-                candidateMap.set(lastSegment, {
+                const item = {
                     canonical: full,
                     scoped,
                     namespace,
-                })
+                }
+                addCandidate(lastSegment, item)
                 if (ignoreCase) {
-                    candidateMap.set(lastSegment.toLowerCase(), {
-                        canonical: full,
-                        scoped,
-                        namespace,
-                    })
+                    addCandidate(lastSegment.toLowerCase(), item)
                 }
             }
         }
 
         // Register the short path if available
         if (short) {
-            candidateMap.set(short, {
+            addCandidate(short, {
                 canonical: full,
                 scoped,
                 namespace,
@@ -162,20 +175,15 @@ export const buildCandidateTrie = (
                 // If alias equals the shorthand, use alias as canonical; otherwise use "full|alias".
                 const canonicalForAlias
                     = short && alias === short ? alias : `${file.path}|${alias}`
-                if (!candidateMap.has(alias)) {
-                    candidateMap.set(alias, {
-                        canonical: canonicalForAlias,
-                        scoped: file.scoped,
-                        namespace: getTopLevelDirectoryName(file.path, baseDir),
-                    })
+                const item = {
+                    canonical: canonicalForAlias,
+                    scoped: file.scoped,
+                    namespace: getTopLevelDirectoryName(file.path, baseDir),
                 }
+                addCandidate(alias, item)
                 // Register lowercase version when ignoreCase is enabled
-                if (ignoreCase && !candidateMap.has(alias.toLowerCase())) {
-                    candidateMap.set(alias.toLowerCase(), {
-                        canonical: canonicalForAlias,
-                        scoped: file.scoped,
-                        namespace: getTopLevelDirectoryName(file.path, baseDir),
-                    })
+                if (ignoreCase) {
+                    addCandidate(alias.toLowerCase(), item)
                 }
             }
         }
@@ -187,70 +195,3 @@ export const buildCandidateTrie = (
 
     return { candidateMap, trie }
 }
-
-if (import.meta.vitest) {
-    const { it, expect, describe } = import.meta.vitest
-
-    // Test for getTopLevelDirectoryName
-    describe("getTopLevelDirectoryName", () => {
-        it("should return the first directory after the baseDir", () => {
-            expect(getTopLevelDirectoryName("pages/docs/file", "pages")).toBe(
-                "docs",
-            )
-            expect(getTopLevelDirectoryName("pages/home/readme", "pages")).toBe(
-                "home",
-            )
-        })
-
-        it("should return the first segment if baseDir is not found", () => {
-            expect(getTopLevelDirectoryName("docs/file")).toBe("docs")
-            expect(getTopLevelDirectoryName("home/readme")).toBe("home")
-        })
-    })
-
-    // Test for buildTrie
-    describe("buildTrie", () => {
-        it("should build a Trie with the given words", () => {
-            const words = ["hello", "world", "hi"]
-            const trie = buildTrie(words)
-
-            expect(trie.children.has("h")).toBe(true)
-            expect(trie.children.has("w")).toBe(true)
-            expect(trie.children.get("h")?.children.has("e")).toBe(true)
-            expect(trie.children.get("h")?.children.get("i")?.candidate).toBe(
-                "hi",
-            )
-        })
-    })
-
-    // Test for buildCandidateTrie
-    describe("buildCandidateTrie", () => {
-        it("should build a candidate map and trie", () => {
-            const allFiles: PathAndAliases[] = [
-                {
-                    path: "pages/docs/readme",
-                    scoped: false,
-                    aliases: ["intro"],
-                },
-                {
-                    path: "pages/home/index",
-                    scoped: false,
-                    aliases: [],
-                },
-            ]
-
-            const { candidateMap, trie } = buildCandidateTrie(
-                allFiles,
-                "pages",
-            )
-
-            expect(candidateMap.has("pages/docs/readme")).toBe(true)
-            expect(candidateMap.has("docs/readme")).toBe(true)
-            expect(candidateMap.get("intro")?.canonical).toBe(
-                "pages/docs/readme|intro",
-            )
-            expect(trie.children.has("d")).toBe(true)
-            expect(trie.children.has("h")).toBe(true)
-        })
-    })
-}

src/utils/__tests__/resolve-ambiguities.test.ts

@@ -0,0 +1,291 @@
+import { describe, it, expect, vi } from "vitest"
+
+vi.mock("obsidian", () => ({
+    request: vi.fn(),
+}))
+
+import { resolveAmbiguities } from "../resolve-ambiguities"
+import { CandidateData, TrieNode, buildTrie } from "../../trie"
+import { AutomaticLinkerSettings, DEFAULT_SETTINGS } from "../../settings/settings-info"
+import * as aiClient from "../ai-client"
+
+vi.mock("../ai-client", () => ({
+    callAI: vi.fn(),
+    resolveAmbiguitiesBatch: vi.fn(),
+}))
+
+describe("resolveAmbiguities", () => {
+    const mockSettings: AutomaticLinkerSettings = {
+        ...DEFAULT_SETTINGS,
+        aiMaxContext: 50,
+    }
+
+    const candidateMap = new Map<string, CandidateData>([
+        [
+            "meeting",
+            {
+                candidates: [
+                    { canonical: "work/meeting", scoped: false, namespace: "work" },
+                    { canonical: "private/meeting", scoped: false, namespace: "private" },
+                ],
+            },
+        ],
+    ])
+
+    const trie: TrieNode = buildTrie(["meeting"], true)
+
+    it("should identify ambiguous unlinked words", async () => {
+        const text = "I have a meeting tomorrow."
+        vi.mocked(aiClient.resolveAmbiguitiesBatch).mockResolvedValue(
+            new Map([["meeting", "work/meeting"]]),
+        )
+
+        const result = await resolveAmbiguities(text, candidateMap, trie, mockSettings)
+
+        expect(aiClient.resolveAmbiguitiesBatch).toHaveBeenCalledWith(
+            mockSettings,
+            expect.arrayContaining([
+                expect.objectContaining({
+                    word: "meeting",
+                    candidates: ["work/meeting", "private/meeting"],
+                }),
+            ]),
+        )
+        expect(result.get("meeting")).toBe("work/meeting")
+    })
+
+    it("should identify ambiguous existing links for verification", async () => {
+        const text = "Check the [[private/meeting|meeting]] notes."
+        vi.mocked(aiClient.resolveAmbiguitiesBatch).mockResolvedValue(
+            new Map([["[[private/meeting|meeting]]", "work/meeting"]]),
+        )
+
+        const result = await resolveAmbiguities(text, candidateMap, trie, mockSettings)
+
+        expect(aiClient.resolveAmbiguitiesBatch).toHaveBeenCalledWith(
+            mockSettings,
+            expect.arrayContaining([
+                expect.objectContaining({
+                    word: "[[private/meeting|meeting]]",
+                    candidates: ["work/meeting", "private/meeting"],
+                }),
+            ]),
+        )
+        expect(result.get("[[private/meeting|meeting]]")).toBe("work/meeting")
+    })
+
+    it("should not request AI for existing links inside inline code", async () => {
+        const text = "Check the `[[private/meeting|meeting]]` notes."
+        vi.mocked(aiClient.resolveAmbiguitiesBatch).mockClear()
+        vi.mocked(aiClient.resolveAmbiguitiesBatch).mockResolvedValue(new Map())
+
+        const result = await resolveAmbiguities(text, candidateMap, trie, mockSettings)
+
+        expect(aiClient.resolveAmbiguitiesBatch).toHaveBeenCalledWith(
+            mockSettings,
+            [],
+        )
+        expect(result.size).toBe(0)
+    })
+
+    it("should skip fenced code blocks, callouts, and ignored headings", async () => {
+        const text = `# meeting
+> [!note]
+> meeting
+
+~~~ts
+meeting
+~~~
+
+meeting`
+        vi.mocked(aiClient.resolveAmbiguitiesBatch).mockClear()
+        vi.mocked(aiClient.resolveAmbiguitiesBatch).mockResolvedValue(
+            new Map([["meeting", "work/meeting"]]),
+        )
+
+        await resolveAmbiguities(text, candidateMap, trie, {
+            ...mockSettings,
+            ignoreHeadings: true,
+            proximityBasedLinking: true,
+        })
+
+        expect(aiClient.resolveAmbiguitiesBatch).toHaveBeenCalledTimes(1)
+        expect(aiClient.resolveAmbiguitiesBatch).toHaveBeenCalledWith(
+            expect.objectContaining({
+                ignoreHeadings: true,
+                proximityBasedLinking: true,
+            }),
+            [
+                expect.objectContaining({
+                    word: "meeting",
+                    candidates: ["work/meeting", "private/meeting"],
+                }),
+            ],
+        )
+    })
+
+    it("should not request AI for Korean particle forms that replacement skips", async () => {
+        const koreanCandidateMap = new Map<string, CandidateData>([
+            [
+                "문서",
+                {
+                    candidates: [
+                        { canonical: "work/문서", scoped: false, namespace: "work" },
+                        { canonical: "private/문서", scoped: false, namespace: "private" },
+                    ],
+                },
+            ],
+        ])
+        const koreanTrie: TrieNode = buildTrie(["문서"], true)
+        vi.mocked(aiClient.resolveAmbiguitiesBatch).mockClear()
+        vi.mocked(aiClient.resolveAmbiguitiesBatch).mockResolvedValue(new Map())
+
+        const result = await resolveAmbiguities(
+            "문서는 문서은",
+            koreanCandidateMap,
+            koreanTrie,
+            mockSettings,
+        )
+
+        expect(aiClient.resolveAmbiguitiesBatch).toHaveBeenCalledWith(
+            mockSettings,
+            [],
+        )
+        expect(result.size).toBe(0)
+    })
+
+    it("should not request AI for self-link candidates when the file path matches", async () => {
+        const selfLinkCandidateMap = new Map<string, CandidateData>([
+            [
+                "meeting",
+                {
+                    candidates: [
+                        { canonical: "work/meeting", scoped: false, namespace: "work" },
+                        { canonical: "private/meeting", scoped: false, namespace: "private" },
+                    ],
+                },
+            ],
+        ])
+        const selfLinkTrie: TrieNode = buildTrie(["meeting"], true)
+        vi.mocked(aiClient.resolveAmbiguitiesBatch).mockClear()
+        vi.mocked(aiClient.resolveAmbiguitiesBatch).mockResolvedValue(new Map())
+
+        const result = await resolveAmbiguities(
+            "meeting",
+            selfLinkCandidateMap,
+            selfLinkTrie,
+            {
+                ...mockSettings,
+                preventSelfLinking: true,
+            },
+            "work/meeting",
+        )
+
+        expect(aiClient.resolveAmbiguitiesBatch).toHaveBeenCalledWith(
+            expect.objectContaining({
+                preventSelfLinking: true,
+            }),
+            [],
+        )
+        expect(result.size).toBe(0)
+    })
+
+    it("uses baseDir when filtering scoped candidates for AI requests", async () => {
+        const scopedCandidateMap = new Map<string, CandidateData>([
+            [
+                "internal",
+                {
+                    candidates: [
+                        { canonical: "pages/team-a/internal", scoped: true, namespace: "team-a" },
+                        { canonical: "pages/team-a/archive/internal", scoped: true, namespace: "team-a" },
+                    ],
+                },
+            ],
+        ])
+        const scopedTrie: TrieNode = buildTrie(["internal"], true)
+        vi.mocked(aiClient.resolveAmbiguitiesBatch).mockClear()
+        vi.mocked(aiClient.resolveAmbiguitiesBatch).mockResolvedValue(new Map())
+
+        await resolveAmbiguities(
+            "internal",
+            scopedCandidateMap,
+            scopedTrie,
+            {
+                ...mockSettings,
+                proximityBasedLinking: true,
+            },
+            "pages/team-a/today",
+            "pages",
+        )
+
+        const [settingsArg, requestsArg] = vi.mocked(aiClient.resolveAmbiguitiesBatch).mock.calls[0]
+        expect(settingsArg).toEqual(expect.objectContaining({
+            proximityBasedLinking: true,
+        }))
+        expect(settingsArg).not.toHaveProperty("baseDir")
+        expect(requestsArg).toEqual([
+            expect.objectContaining({
+                word: "internal",
+                candidates: [
+                    "pages/team-a/internal",
+                    "pages/team-a/archive/internal",
+                ],
+            }),
+        ])
+    })
+
+    it("does not request AI for candidates inside raw Linear URLs", async () => {
+        const linearCandidateMap = new Map<string, CandidateData>([
+            [
+                "linear",
+                {
+                    candidates: [
+                        { canonical: "work/linear", scoped: false, namespace: "work" },
+                        { canonical: "private/linear", scoped: false, namespace: "private" },
+                    ],
+                },
+            ],
+        ])
+        const linearTrie: TrieNode = buildTrie(["linear"], true)
+        vi.mocked(aiClient.resolveAmbiguitiesBatch).mockClear()
+        vi.mocked(aiClient.resolveAmbiguitiesBatch).mockResolvedValue(new Map())
+
+        const result = await resolveAmbiguities(
+            "Open linear://issue/TEAM-123",
+            linearCandidateMap,
+            linearTrie,
+            mockSettings,
+        )
+
+        expect(aiClient.resolveAmbiguitiesBatch).toHaveBeenCalledWith(
+            mockSettings,
+            [],
+        )
+        expect(result.size).toBe(0)
+    })
+
+    it("does not request AI for candidates inside ignored Markdown table rows", async () => {
+        vi.mocked(aiClient.resolveAmbiguitiesBatch).mockClear()
+        vi.mocked(aiClient.resolveAmbiguitiesBatch).mockResolvedValue(new Map())
+
+        const result = await resolveAmbiguities(
+            `| Topic |
+| --- |
+| meeting |`,
+            candidateMap,
+            trie,
+            {
+                ...mockSettings,
+                ignoreMarkdownTables: true,
+            },
+        )
+
+        expect(aiClient.resolveAmbiguitiesBatch).toHaveBeenCalledWith(
+            expect.objectContaining({
+                ignoreMarkdownTables: true,
+            }),
+            [],
+        )
+        expect(result.size).toBe(0)
+    })
+})

src/utils/ai-client.ts

@@ -0,0 +1,103 @@
+import { request } from "obsidian"
+import { AutomaticLinkerSettings } from "../settings/settings-info"
+
+export interface AIResolveRequest {
+    text: string
+    word: string
+    candidates: string[]
+}
+
+export interface AIResolveResponse {
+    selectedPath: string | null
+}
+
+export const callAI = async (
+    settings: AutomaticLinkerSettings,
+    prompt: string,
+): Promise<string> => {
+    const url = `${settings.aiEndpoint}/chat/completions`
+    const body = {
+        model: settings.aiModel,
+        messages: [
+            {
+                role: "system",
+                content: "You are an assistant that helps resolve ambiguous links in Obsidian notes. You must respond ONLY with a valid JSON object. Do not include any explanation or markdown code blocks.",
+            },
+            {
+                role: "user",
+                content: prompt,
+            },
+        ],
+        // Some local servers fail with response_format, so we rely on the prompt instructions
+        // temperature: 0 to make it more deterministic
+        temperature: 0,
+    }
+
+    if (settings.debug) {
+        console.log("AI Link Enhancer Request:", JSON.stringify(body, null, 2))
+    }
+
+    try {
+        const response = await request({
+            url,
+            method: "POST",
+            headers: {
+                "Content-Type": "application/json",
+            },
+            body: JSON.stringify(body),
+        })
+
+        if (settings.debug) {
+            console.log("AI Link Enhancer Response:", response)
+        }
+
+        const data = JSON.parse(response)
+        return data.choices[0].message.content
+    }
+    catch (error) {
+        console.error("AI Link Enhancer API Error:", error)
+        throw error
+    }
+}
+
+export const resolveAmbiguitiesBatch = async (
+    settings: AutomaticLinkerSettings,
+    requests: AIResolveRequest[],
+): Promise<Map<string, string>> => {
+    if (requests.length === 0) return new Map()
+
+    const prompt = `
+Please resolve the following ambiguous links.
+Select the most appropriate "selectedPath" from the given "candidates" based on the context.
+If no candidate is appropriate, return null for that item.
+
+You MUST respond with a JSON object in the following format:
+{
+  "results": [
+    { "word": "word1", "selectedPath": "path/to/note" },
+    ...
+  ]
+}
+
+Input data:
+${JSON.stringify(requests, null, 2)}
+`
+
+    const resultRaw = await callAI(settings, prompt)
+
+    // Clean up potential markdown code blocks if the AI included them
+    const cleanJson = resultRaw.replace(/```json\n?/, "").replace(/\n?```/, "").trim()
+
+    const result = JSON.parse(cleanJson)
+    const resultMap = new Map<string, string>()
+
+    if (result.results && Array.isArray(result.results)) {
+        for (const item of result.results) {
+            if (item.selectedPath) {
+                resultMap.set(item.word, item.selectedPath)
+            }
+        }
+    }
+
+    return resultMap
+}

src/utils/resolve-ambiguities.ts

@@ -0,0 +1,39 @@
+import { CandidateData, TrieNode } from "../trie"
+import { AutomaticLinkerSettings } from "../settings/settings-info"
+import { resolveAmbiguitiesBatch, AIResolveRequest } from "./ai-client"
+import {
+    getOccurrenceContext,
+    scanCandidateOccurrences,
+} from "../replace-links/candidate-scanner"
+
+export const resolveAmbiguities = async (
+    text: string,
+    candidateMap: Map<string, CandidateData>,
+    trie: TrieNode,
+    settings: AutomaticLinkerSettings,
+    filePath = "",
+    baseDir?: string,
+): Promise<Map<string, string>> => {
+    const scannerSettings = baseDir === undefined
+        ? settings
+        : { ...settings, baseDir }
+    const occurrences = scanCandidateOccurrences({
+        text,
+        filePath,
+        trie,
+        candidateMap,
+        settings: scannerSettings,
+    })
+
+    const requests: AIResolveRequest[] = occurrences
+        .filter(occurrence => occurrence.candidateData.candidates.length > 1)
+        .map(occurrence => ({
+            word: occurrence.text,
+            text: getOccurrenceContext(text, occurrence, settings.aiMaxContext),
+            candidates: occurrence.candidateData.candidates.map(c => c.canonical),
+        }))
+
+    const uniqueRequests = Array.from(new Map(requests.map(r => [r.word, r])).values())
+
+    return await resolveAmbiguitiesBatch(settings, uniqueRequests)
+}

versions.json

@@ -100,5 +100,28 @@
 	"3.1.2": "1.9.0",
 	"3.2.0": "1.9.0",
 	"3.2.1": "1.9.0",
-	"4.0.0": "1.9.0"
+	"4.0.0": "1.9.0",
+	"4.0.1": "1.9.0",
+	"4.0.2": "1.9.0",
+	"4.0.3": "1.9.0",
+	"4.0.4": "1.9.0",
+	"4.0.5": "1.9.0",
+	"4.1.0": "1.9.0",
+	"4.1.1": "1.9.0",
+	"4.1.2": "1.9.0",
+	"4.1.3": "1.9.0",
+	"4.2.0": "1.9.0",
+	"4.3.0": "1.9.0",
+	"4.3.1": "1.9.0",
+	"4.3.2": "1.9.0",
+	"4.3.3": "1.9.0",
+	"4.4.0": "1.9.0",
+	"4.5.0": "1.9.0",
+	"4.5.1": "1.9.0",
+	"4.5.2": "1.9.0",
+	"4.5.3": "1.9.0",
+	"4.6.0": "1.9.0",
+	"4.7.0": "1.9.0",
+	"4.7.1": "1.9.0",
+	"4.7.2": "1.9.0"
 }

vitest.config.ts

@@ -1,7 +1,11 @@
 import { defineConfig } from "vitest/config"
+import path from "path"
 
 export default defineConfig({
     test: {
         includeSource: ["src/**/*.{js,ts}"],
+        alias: {
+            obsidian: path.resolve(__dirname, "./src/__mocks__/obsidian.ts"),
+        },
     },
 })