fix(formatting): restore selection-only link replacement

Why:
- The selection command regressed by inheriting document-level URL formatting from the shared body formatter.
- That changed user-visible output for selected text containing GitHub, Jira, or Linear URLs.

What:
- Added a selection-only formatter that projects link replacement settings and calls `replaceLinks(...)` directly.
- Switched `mofifyLinksSelection()` to the new helper so document formatting stays unchanged.
- Added regression coverage for selection-only behavior and documented the fix in the task report.

.superpowers/sdd/task-2-report.md

@@ -83,3 +83,49 @@ Results:
 ## Concerns
 
 None.
+
+## Fix: Selection Formatting Regression
+
+Selection formatting was accidentally routed through `formatMarkdownBody(...)`, which let URL-formatting behavior leak into the selection command.
+
+### RED
+
+Command:
+
+```bash
+npx vitest run src/__tests__/main-link-generator.test.ts
+```
+
+Result:
+
+- Failed as expected
+- Failure showed `mofifyLinksSelection()` was formatting a GitHub URL instead of leaving it unchanged:
+  `[[notes/TypeScript|TypeScript]] [[github/openai/openai/issues/1]] [🔗](https://github.com/openai/openai/issues/1)`
+
+### GREEN
+
+Changes:
+
+- Added `formatMarkdownSelection(...)` in `src/formatting-run.ts`
+- Updated `mofifyLinksSelection()` in `src/main.ts` to call the selection-only helper
+- Added a unit guard in `src/__tests__/formatting-run.test.ts`
+
+### Verification
+
+Commands:
+
+```bash
+npx vitest run src/__tests__/formatting-run.test.ts src/__tests__/main-link-generator.test.ts
+npm run tsc
+npm run lint
+```
+
+Results:
+
+- `npx vitest run src/__tests__/formatting-run.test.ts src/__tests__/main-link-generator.test.ts`: passed `2` files, `7` tests
+- `npm run tsc`: exit `0`
+- `npm run lint`: exit `0`
+
+### Concerns
+
+- Selection formatting now has its own helper; any future selection-specific behavior should be added there, not to `formatMarkdownBody(...)`.

src/__tests__/formatting-run.test.ts

@@ -2,6 +2,7 @@ import { describe, expect, it } from "vitest"
 import {
     formatMarkdownBody,
     formatMarkdownDocument,
+    formatMarkdownSelection,
     toReplaceLinksSettings,
 } from "../formatting-run"
 import { buildCandidateTrieForTest } from "../replace-links/__tests__/test-helpers"
@@ -111,3 +112,34 @@ describe("formatMarkdownBody", () => {
         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",
+        )
+    })
+})

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

@@ -76,4 +76,56 @@ describe("AutomaticLinkerPlugin link generator", () => {
 
         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/formatting-run.ts

@@ -84,6 +84,30 @@ export const formatMarkdownBody = ({
     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: toReplaceLinksSettings(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

src/main.ts

@@ -12,8 +12,8 @@ import {
 } from "obsidian"
 import { excludeLinks } from "./exclude-links"
 import {
-    formatMarkdownBody,
     formatMarkdownDocument,
+    formatMarkdownSelection,
     toReplaceLinksSettings,
 } from "./formatting-run"
 import {
@@ -233,7 +233,7 @@ export default class AutomaticLinkerPlugin extends Plugin {
 
         const linkGenerator = this.createLinkGenerator(activeFile.path)
         const baseDir = this.settings.respectNewFileFolderPath ? this.app.vault.getConfig("newFileFolderPath") : undefined
-        const updatedText = formatMarkdownBody({
+        const updatedText = formatMarkdownSelection({
             body: selectedText,
             filePath: activeFile.path,
             settings: this.settings,