fix: restore raw URL helper semantics

Why: Task 5 centralized URL formatting but accidentally changed shared Markdown segmentation and the legacy replaceURLs compatibility path.

What: remove angle-bracket autolink protection from shared segmentation, keep angle-bracket and trailing-punctuation handling inside formatURLsInText, and restore replaceURLs to a direct regex replace with linear:// support.

src/__tests__/markdown-segments.test.ts

@@ -74,12 +74,12 @@ describe("mapMarkdownProse", () => {
         expect(result).toBe("TS `TypeScript` [[TypeScript]]")
     })
 
-    it("treats angle-bracket autolinks as protected segments", () => {
+    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("<https://example.com> URL")
+        expect(result).toBe("<URL> URL")
     })
 })

src/markdown-segments.ts

@@ -132,7 +132,6 @@ const collectFencedCodeRanges = (text: string): ProtectedRange[] => {
 const buildProtectedPattern = (protectUrls: boolean): RegExp => {
     const parts = [
         "`[^`]*`",
-        "<(?:https?:\\/\\/|linear:\\/\\/)[^>]+>",
         "\\[\\[[^\\]]+\\]\\]",
         "\\[[^\\]]+\\]\\([^)]+\\)",
         "\\[[^\\]]+\\]",
@@ -197,7 +196,6 @@ export const segmentMarkdown = (
 ): MarkdownSegment[] => {
     const mayContainProtectedMarkdown = text.includes("`")
         || text.includes("~")
-        || text.includes("<")
         || text.includes("[")
         || (options.protectHeadings && text.includes("#"))
         || (options.protectCallouts && text.includes(">"))

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

@@ -14,8 +14,7 @@ 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(
@@ -39,4 +38,24 @@ describe("replace-urls", () => {
             ),
         ).toBe(expected)
     })
+
+    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

@@ -60,6 +60,18 @@ describe("formatURLsInText", () => {
         ].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",
@@ -72,6 +84,35 @@ describe("formatURLsInText", () => {
         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: [

src/replace-urls/replace-urls.ts

@@ -1,4 +1,3 @@
-import { mapMarkdownProse } from "../markdown-segments"
 import { AutomaticLinkerSettings } from "../settings/settings-info"
 
 const URL_PATTERN = /(?:https?:\/\/|linear:\/\/)[^\s<>\]]+/g
@@ -7,8 +6,4 @@ export const replaceURLs = (
     fileContent: string,
     settings: AutomaticLinkerSettings,
     formatter: (url: string, settings: AutomaticLinkerSettings) => string,
-) =>
-    mapMarkdownProse(
-        fileContent,
-        prose => prose.replace(URL_PATTERN, match => formatter(match, settings)),
-    )
+) => fileContent.replace(URL_PATTERN, match => formatter(match, settings))

src/replace-urls/url-formatting.ts

@@ -26,6 +26,48 @@ const formatJiraURLIfEnabled: UrlFormatter = (url, settings) =>
 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,
@@ -54,8 +96,19 @@ export const formatURLsInText = ({
 }: FormatURLsInTextOptions): string =>
     mapMarkdownProse(
         text,
-        prose =>
-            prose.replace(URL_PATTERN, match =>
-                formatURLWithAdapters(match, settings, formatters),
-            ),
+        (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
+            }),
     )