[codex] Refine markdown issue reference rendering (#4382)

## Thinking Path

> - Paperclip orchestrates AI agents for zero-human companies
> - Task references are a core part of how operators understand issue
relationships across the UI
> - Those references appear both in markdown bodies and in sidebar
relationship panels
> - The rendering had drifted between surfaces, and inline markdown
pills were reading awkwardly inside prose and lists
> - This pull request unifies the underlying issue-reference treatment,
routes issue descriptions through `MarkdownBody`, and switches inline
markdown references to a cleaner text-link presentation
> - The benefit is more consistent issue-reference UX with better
readability in markdown-heavy views

## What Changed

- unified sidebar and markdown issue-reference rendering around the
shared issue-reference components
- routed resting issue descriptions through `MarkdownBody` so
description previews inherit the richer issue-reference treatment
- replaced inline markdown pill chrome with a cleaner inline reference
presentation for prose contexts
- added and updated UI tests for `MarkdownBody` and `InlineEditor`

## Verification

- `pnpm exec vitest run --project @paperclipai/ui
ui/src/components/MarkdownBody.test.tsx
ui/src/components/InlineEditor.test.tsx`

## Risks

- Moderate UI risk: issue-reference rendering now differs intentionally
between inline markdown and relationship sidebars, so regressions would
show up as styling or hover-preview mismatches

> For core feature work, check [`ROADMAP.md`](ROADMAP.md) first and
discuss it in `#dev` before opening the PR. Feature PRs that overlap
with planned core work may need to be redirected — check the roadmap
first. See `CONTRIBUTING.md`.

## Model Used

- OpenAI Codex GPT-5-based coding agent with tool use and code execution
in the Codex CLI environment

## Checklist

- [x] I have included a thinking path that traces from project context
to this change
- [x] I have specified the model used (with version and capability
details)
- [x] I have checked ROADMAP.md and confirmed this PR does not duplicate
planned core work
- [x] I have run tests locally and they pass
- [x] I have added or updated tests where applicable
- [ ] If this change affects the UI, I have included before/after
screenshots
- [ ] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] I will address all Greptile and reviewer comments before
requesting merge

---------

Co-authored-by: Paperclip <noreply@paperclip.ing>

ui/src/lib/issue-reference.test.ts

@@ -4,6 +4,7 @@ import { parseIssuePathIdFromPath, parseIssueReferenceFromHref } from "./issue-r
 describe("issue-reference", () => {
   it("extracts issue ids from company-scoped issue paths", () => {
     expect(parseIssuePathIdFromPath("/PAP/issues/PAP-1271")).toBe("PAP-1271");
+    expect(parseIssuePathIdFromPath("/PAP/issues/pap-1272")).toBe("PAP-1272");
     expect(parseIssuePathIdFromPath("/issues/PAP-1179")).toBe("PAP-1179");
     expect(parseIssuePathIdFromPath("/issues/:id")).toBeNull();
   });
@@ -32,6 +33,10 @@ describe("issue-reference", () => {
       issuePathId: "PAP-1179",
       href: "/issues/PAP-1179",
     });
+    expect(parseIssueReferenceFromHref("/PAP/issues/pap-1180")).toEqual({
+      issuePathId: "PAP-1180",
+      href: "/issues/PAP-1180",
+    });
     expect(parseIssueReferenceFromHref("issue://PAP-1310")).toEqual({
       issuePathId: "PAP-1310",
       href: "/issues/PAP-1310",

ui/src/lib/issue-reference.ts

@@ -7,7 +7,7 @@ type MarkdownNode = {
 
 const BARE_ISSUE_IDENTIFIER_RE = /^[A-Z][A-Z0-9]+-\d+$/i;
 const ISSUE_SCHEME_RE = /^issue:\/\/:?([^?#\s]+)(?:[?#].*)?$/i;
-const ISSUE_REFERENCE_TOKEN_RE = /issue:\/\/:?[^\s<>()]+|https?:\/\/[^\s<>()]+|\b[A-Z][A-Z0-9]+-\d+\b/gi;
+const ISSUE_REFERENCE_TOKEN_RE = /issue:\/\/:?[^\s<>()]+|https?:\/\/[^\s<>()]+|\/(?:[^\s<>()/]+\/)*issues\/[A-Z][A-Z0-9]+-\d+(?=$|[\s<>)\],.;!?:])|\b[A-Z][A-Z0-9]+-\d+\b/gi;
 
 export function parseIssuePathIdFromPath(pathOrUrl: string | null | undefined): string | null {
   if (!pathOrUrl) return null;
@@ -29,7 +29,7 @@ export function parseIssuePathIdFromPath(pathOrUrl: string | null | undefined):
   if (issueIndex === -1 || issueIndex === segments.length - 1) return null;
   const issuePathId = decodeURIComponent(segments[issueIndex + 1] ?? "");
   if (!issuePathId || issuePathId.startsWith(":")) return null;
-  return issuePathId;
+  return BARE_ISSUE_IDENTIFIER_RE.test(issuePathId) ? issuePathId.toUpperCase() : issuePathId;
 }
 
 export function parseIssueReferenceFromHref(href: string | null | undefined) {
@@ -66,12 +66,17 @@ function splitTrailingPunctuation(token: string) {
 
   while (core.length > 0) {
     const lastChar = core.at(-1);
-    if (!lastChar || !/[),.;!?]/.test(lastChar)) break;
+    if (!lastChar || !/[),.;!?:\]]/.test(lastChar)) break;
     if (lastChar === ")") {
       const openCount = (core.match(/\(/g) ?? []).length;
       const closeCount = (core.match(/\)/g) ?? []).length;
       if (closeCount <= openCount) break;
     }
+    if (lastChar === "]") {
+      const openCount = (core.match(/\[/g) ?? []).length;
+      const closeCount = (core.match(/\]/g) ?? []).length;
+      if (closeCount <= openCount) break;
+    }
     trailing = `${lastChar}${trailing}`;
     core = core.slice(0, -1);
   }