[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/components/InlineEditor.test.tsx

@@ -1,6 +1,6 @@
 // @vitest-environment jsdom
 
-import { act, forwardRef, useImperativeHandle, useRef } from "react";
+import { act, forwardRef, useImperativeHandle, useRef, type ReactNode } from "react";
 import { createRoot } from "react-dom/client";
 import { afterEach, beforeEach, describe, expect, it, vi } from "vitest";
 
@@ -24,8 +24,22 @@ vi.mock("./MarkdownEditor", () => ({
   }),
 }));
 
+vi.mock("./MarkdownBody", () => ({
+  MarkdownBody: ({ children }: { children: ReactNode }) => (
+    <div data-testid="multiline-md-preview">{children}</div>
+  ),
+}));
+
 import { InlineEditor, queueContainedBlurCommit } from "./InlineEditor";
 
+/** Enter multiline edit mode by clicking the preview surface. */
+function enterMultilineEdit(container: HTMLDivElement) {
+  const preview = container.querySelector<HTMLDivElement>('[data-testid="multiline-md-preview"]');
+  if (preview) {
+    preview.dispatchEvent(new MouseEvent("click", { bubbles: true }));
+  }
+}
+
 // eslint-disable-next-line @typescript-eslint/no-explicit-any
 (globalThis as any).IS_REACT_ACT_ENVIRONMENT = true;
 
@@ -139,6 +153,11 @@ describe("InlineEditor", () => {
       root.render(<InlineEditor value="hello" multiline nullable onSave={onSave} />);
     });
 
+    // Non-empty value renders MarkdownBody preview; click to enter edit mode.
+    act(() => {
+      enterMultilineEdit(container);
+    });
+
     const textarea = container.querySelector<HTMLTextAreaElement>('[data-testid="multiline-md-mock"]');
     expect(textarea).not.toBeNull();
 
@@ -165,6 +184,70 @@ describe("InlineEditor", () => {
     outside.remove();
   });
 
+  it("multiline defaults to MarkdownBody preview when value is non-empty, swaps to editor on click", () => {
+    const onSave = vi.fn().mockResolvedValue(undefined);
+    const root = createRoot(container);
+
+    act(() => {
+      root.render(<InlineEditor value="Hello world" multiline onSave={onSave} />);
+    });
+
+    expect(container.querySelector('[data-testid="multiline-md-preview"]')).not.toBeNull();
+    expect(container.querySelector('[data-testid="multiline-md-mock"]')).toBeNull();
+
+    act(() => {
+      enterMultilineEdit(container);
+    });
+
+    expect(container.querySelector('[data-testid="multiline-md-mock"]')).not.toBeNull();
+    expect(container.querySelector('[data-testid="multiline-md-preview"]')).toBeNull();
+
+    act(() => {
+      root.unmount();
+    });
+  });
+
+  it("marks multiline preview textboxes as multiline", () => {
+    const onSave = vi.fn().mockResolvedValue(undefined);
+    const root = createRoot(container);
+
+    act(() => {
+      root.render(<InlineEditor value="Hello world" multiline onSave={onSave} />);
+    });
+
+    const preview = container.querySelector<HTMLElement>('[role="textbox"]');
+    expect(preview).not.toBeNull();
+    expect(preview?.getAttribute("aria-multiline")).toBe("true");
+    expect(preview?.tabIndex).toBe(0);
+
+    act(() => {
+      root.unmount();
+    });
+  });
+
+  it("enters multiline edit mode from the keyboard preview surface", () => {
+    const onSave = vi.fn().mockResolvedValue(undefined);
+    const root = createRoot(container);
+
+    act(() => {
+      root.render(<InlineEditor value="Hello world" multiline onSave={onSave} />);
+    });
+
+    const preview = container.querySelector<HTMLElement>('[role="textbox"]');
+    expect(preview).not.toBeNull();
+
+    act(() => {
+      preview!.dispatchEvent(new KeyboardEvent("keydown", { bubbles: true, key: "Enter" }));
+    });
+
+    expect(container.querySelector('[data-testid="multiline-md-mock"]')).not.toBeNull();
+    expect(container.querySelector('[data-testid="multiline-md-preview"]')).toBeNull();
+
+    act(() => {
+      root.unmount();
+    });
+  });
+
   it("syncs a new multiline value while focused when the user has not edited locally", () => {
     const onSave = vi.fn().mockResolvedValue(undefined);
     const root = createRoot(container);
@@ -200,6 +283,11 @@ describe("InlineEditor", () => {
       root.render(<InlineEditor value="Original" multiline onSave={onSave} />);
     });
 
+    // Non-empty value renders MarkdownBody preview; click to enter edit mode.
+    act(() => {
+      enterMultilineEdit(container);
+    });
+
     const textarea = container.querySelector<HTMLTextAreaElement>('[data-testid="multiline-md-mock"]');
     expect(textarea).not.toBeNull();
 

ui/src/components/InlineEditor.tsx

@@ -1,5 +1,6 @@
 import { useState, useRef, useEffect, useCallback } from "react";
 import { cn } from "../lib/utils";
+import { MarkdownBody } from "./MarkdownBody";
 import { MarkdownEditor, type MarkdownEditorRef, type MentionOption } from "./MarkdownEditor";
 import { useAutosaveIndicator } from "../hooks/useAutosaveIndicator";
 
@@ -52,6 +53,7 @@ export function InlineEditor({
   mentions,
 }: InlineEditorProps) {
   const [editing, setEditing] = useState(false);
+  const [multilineEditing, setMultilineEditing] = useState(false);
   const [multilineFocused, setMultilineFocused] = useState(false);
   const [draft, setDraft] = useState(value);
   const lastPropValueRef = useRef(value);
@@ -59,6 +61,9 @@ export function InlineEditor({
   const markdownRef = useRef<MarkdownEditorRef>(null);
   const autosaveDebounceRef = useRef<ReturnType<typeof setTimeout> | null>(null);
   const blurCommitFrameRef = useRef<(() => void) | null>(null);
+  const pendingFocusFrameRef = useRef<number | null>(null);
+  const justEnteredEditRef = useRef(false);
+  const hasBeenFocusedRef = useRef(false);
   const {
     state: autosaveState,
     markDirty,
@@ -86,6 +91,10 @@ export function InlineEditor({
         blurCommitFrameRef.current();
         blurCommitFrameRef.current = null;
       }
+      if (pendingFocusFrameRef.current !== null) {
+        cancelAnimationFrame(pendingFocusFrameRef.current);
+        pendingFocusFrameRef.current = null;
+      }
     };
   }, []);
 
@@ -106,12 +115,39 @@ export function InlineEditor({
   }, [editing, autoSize]);
 
   useEffect(() => {
-    if (!editing || !multiline) return;
+    if (!multilineEditing || !multiline) return;
-    const frame = requestAnimationFrame(() => {
+    if (!justEnteredEditRef.current) return;
+    justEnteredEditRef.current = false;
+    if (pendingFocusFrameRef.current !== null) {
+      cancelAnimationFrame(pendingFocusFrameRef.current);
+    }
+    pendingFocusFrameRef.current = requestAnimationFrame(() => {
+      pendingFocusFrameRef.current = null;
       markdownRef.current?.focus();
     });
-    return () => cancelAnimationFrame(frame);
+    return () => {
-  }, [editing, multiline]);
+      if (pendingFocusFrameRef.current !== null) {
+        cancelAnimationFrame(pendingFocusFrameRef.current);
+        pendingFocusFrameRef.current = null;
+      }
+    };
+  }, [multilineEditing, multiline]);
+
+  // Once the editor has been focused at least once, it's blurred, and any
+  // autosave has settled, swap back to the MarkdownBody preview so inline
+  // issue refs render with status + quicklook.
+  useEffect(() => {
+    if (multilineFocused) {
+      hasBeenFocusedRef.current = true;
+      return;
+    }
+    if (!multiline || !multilineEditing) return;
+    if (!hasBeenFocusedRef.current) return;
+    if (autosaveState !== "idle") return;
+    hasBeenFocusedRef.current = false;
+    setMultilineEditing(false);
+  }, [multiline, multilineEditing, multilineFocused, autosaveState]);
+
 
   const commit = useCallback(async (nextValue = draft) => {
     const valueToSave = nextValue.trim();
@@ -176,6 +212,8 @@ export function InlineEditor({
       setDraft(value);
       if (multiline) {
         setMultilineFocused(false);
+        setMultilineEditing(false);
+        hasBeenFocusedRef.current = false;
         if (document.activeElement instanceof HTMLElement) {
           document.activeElement.blur();
         }
@@ -212,6 +250,45 @@ export function InlineEditor({
   }, [autosaveState, commit, draft, markDirty, multiline, multilineFocused, nullable, reset, runSave, value]);
 
   if (multiline) {
+    const previewValue = autosaveState === "saved" || autosaveState === "idle" ? draft : value;
+    const hasValue = Boolean(previewValue.trim());
+    const showEditor = multilineEditing || multilineFocused || !hasValue;
+
+    if (!showEditor) {
+      const enterEditMode = () => {
+        if (multilineEditing) return;
+        justEnteredEditRef.current = true;
+        setMultilineEditing(true);
+      };
+      return (
+        <div
+          className={cn(markdownPad, "rounded transition-colors hover:bg-accent/20")}
+          onClick={(event) => {
+            if (event.defaultPrevented) return;
+            const target = event.target as HTMLElement | null;
+            if (target && target.closest("a,button,[data-mention-kind],[data-radix-popper-content-wrapper]")) {
+              return;
+            }
+            enterEditMode();
+          }}
+          onDragEnter={() => enterEditMode()}
+          onKeyDown={(event) => {
+            if (event.key !== "Enter" && event.key !== " ") return;
+            event.preventDefault();
+            enterEditMode();
+          }}
+          role="textbox"
+          aria-multiline="true"
+          aria-label={placeholder}
+          tabIndex={0}
+        >
+          <MarkdownBody className={cn("paperclip-edit-in-place-content", className)}>
+            {previewValue}
+          </MarkdownBody>
+        </div>
+      );
+    }
+
     return (
       <div
         className={cn(
@@ -219,12 +296,20 @@ export function InlineEditor({
           "rounded transition-colors",
           multilineFocused ? "bg-transparent" : "hover:bg-accent/20",
         )}
-        onFocusCapture={() => {
+        onFocusCapture={(event) => {
+          // Ignore focus events where the active element isn't actually inside
+          // the wrapper (React 19 can emit a synthetic focus after a blur).
+          const active = document.activeElement;
+          if (!(active instanceof Node) || !event.currentTarget.contains(active)) return;
           cancelPendingBlurCommit();
           setMultilineFocused(true);
         }}
         onBlurCapture={(event) => {
           if (event.currentTarget.contains(event.relatedTarget as Node | null)) return;
+          if (pendingFocusFrameRef.current !== null) {
+            cancelAnimationFrame(pendingFocusFrameRef.current);
+            pendingFocusFrameRef.current = null;
+          }
           scheduleBlurCommit(event.currentTarget);
         }}
         onKeyDown={handleKeyDown}

ui/src/components/IssueProperties.tsx

@@ -1,7 +1,7 @@
 import { useCallback, useEffect, useMemo, useRef, useState } from "react";
 import { pickTextColorForPillBg } from "@/lib/color-contrast";
 import { Link } from "@/lib/router";
-import type { Issue, IssueLabel, IssueRelationIssueSummary, Project, WorkspaceRuntimeService } from "@paperclipai/shared";
+import type { Issue, IssueLabel, Project, WorkspaceRuntimeService } from "@paperclipai/shared";
 import { useMutation, useQuery, useQueryClient } from "@tanstack/react-query";
 import { accessApi } from "../api/access";
 import { agentsApi } from "../api/agents";
@@ -197,21 +197,6 @@ function PropertyPicker({
   );
 }
 
-function IssuePillLink({
-  issue,
-}: {
-  issue: Pick<Issue, "id" | "identifier" | "title"> | IssueRelationIssueSummary;
-}) {
-  return (
-    <Link
-      to={`/issues/${issue.identifier ?? issue.id}`}
-      className="inline-flex max-w-full items-center rounded-full border border-border px-2 py-0.5 text-xs hover:bg-accent/50"
-    >
-      <span className="truncate">{issue.identifier ?? issue.title}</span>
-    </Link>
-  );
-}
-
 export function IssueProperties({
   issue,
   childIssues = [],
@@ -1146,7 +1131,7 @@ export function IssueProperties({
           <div>
             <PropertyRow label="Blocked by">
               {(issue.blockedBy ?? []).map((relation) => (
-                <IssuePillLink key={relation.id} issue={relation} />
+                <IssueReferencePill key={relation.id} issue={relation} />
               ))}
               {renderAddBlockedByButton(() => setBlockedByOpen((open) => !open))}
             </PropertyRow>
@@ -1159,7 +1144,7 @@ export function IssueProperties({
         ) : (
           <PropertyRow label="Blocked by">
             {(issue.blockedBy ?? []).map((relation) => (
-              <IssuePillLink key={relation.id} issue={relation} />
+              <IssueReferencePill key={relation.id} issue={relation} />
             ))}
             <Popover
               open={blockedByOpen}
@@ -1182,7 +1167,7 @@ export function IssueProperties({
           {blockingIssues.length > 0 ? (
             <div className="flex flex-wrap gap-1">
               {blockingIssues.map((relation) => (
-                <IssuePillLink key={relation.id} issue={relation} />
+                <IssueReferencePill key={relation.id} issue={relation} />
               ))}
             </div>
           ) : null}
@@ -1192,7 +1177,7 @@ export function IssueProperties({
           <div className="flex flex-wrap items-center gap-1.5">
             {childIssues.length > 0
               ? childIssues.map((child) => (
-                <IssuePillLink key={child.id} issue={child} />
+                <IssueReferencePill key={child.id} issue={child} />
               ))
               : null}
             {onAddSubIssue ? (

ui/src/components/IssueReferencePill.tsx

@@ -1,3 +1,4 @@
+import type { ReactNode } from "react";
 import type { IssueRelationIssueSummary } from "@paperclipai/shared";
 import { Link } from "@/lib/router";
 import { cn } from "../lib/utils";
@@ -7,11 +8,13 @@ export function IssueReferencePill({
   issue,
   strikethrough,
   className,
+  children,
 }: {
   issue: Pick<IssueRelationIssueSummary, "id" | "identifier" | "title"> &
     Partial<Pick<IssueRelationIssueSummary, "status">>;
   strikethrough?: boolean;
   className?: string;
+  children?: ReactNode;
 }) {
   const issueLabel = issue.identifier ?? issue.title;
   const classNames = cn(
@@ -24,7 +27,7 @@ export function IssueReferencePill({
   const content = (
     <>
       {issue.status ? <StatusIcon status={issue.status} className="h-3 w-3 shrink-0" /> : null}
-      <span>{issue.identifier ?? issue.title}</span>
+      {children !== undefined ? children : <span>{issue.identifier ?? issue.title}</span>}
     </>
   );
 

ui/src/components/MarkdownBody.test.tsx

@@ -33,7 +33,7 @@ vi.mock("../api/issues", () => ({
   issuesApi: mockIssuesApi,
 }));
 
-function renderMarkdown(children: string, seededIssues: Array<{ identifier: string; status: string }> = []) {
+function renderMarkdown(children: string, seededIssues: Array<{ identifier: string; status: string; title?: string }> = []) {
   const queryClient = new QueryClient({
     defaultOptions: {
       queries: {
@@ -47,6 +47,7 @@ function renderMarkdown(children: string, seededIssues: Array<{ identifier: stri
       id: issue.identifier,
       identifier: issue.identifier,
       status: issue.status,
+      title: issue.title,
     });
   }
 
@@ -156,9 +157,22 @@ describe("MarkdownBody", () => {
     expect(html).toContain('href="/issues/PAP-1271"');
     expect(html).toContain("text-green-600");
     expect(html).toContain(">PAP-1271<");
+    expect(html).toContain('data-mention-kind="issue"');
+    expect(html).toContain("paperclip-markdown-issue-ref");
     expect(html).not.toContain("paperclip-mention-chip--issue");
   });
 
+  it("uses concise issue aria labels until a distinct title is available", () => {
+    const html = renderMarkdown("Depends on PAP-1271 and PAP-1272.", [
+      { identifier: "PAP-1271", status: "done" },
+      { identifier: "PAP-1272", status: "blocked", title: "Fix hover state" },
+    ]);
+
+    expect(html).toContain('aria-label="Issue PAP-1271"');
+    expect(html).toContain('aria-label="Issue PAP-1272: Fix hover state"');
+    expect(html).not.toContain('aria-label="Issue PAP-1271: PAP-1271"');
+  });
+
   it("rewrites full issue URLs to internal issue links", () => {
     const html = renderMarkdown("See http://localhost:3100/PAP/issues/PAP-1179.", [
       { identifier: "PAP-1179", status: "blocked" },
@@ -167,9 +181,33 @@ describe("MarkdownBody", () => {
     expect(html).toContain('href="/issues/PAP-1179"');
     expect(html).toContain("text-red-600");
     expect(html).toContain(">http://localhost:3100/PAP/issues/PAP-1179<");
+    expect(html).toContain('data-mention-kind="issue"');
     expect(html).not.toContain("paperclip-mention-chip--issue");
   });
 
+  it("linkifies plain internal issue paths in markdown text", () => {
+    const html = renderMarkdown("See /issues/PAP-1179 and /PAP/issues/pap-1180 for context.", [
+      { identifier: "PAP-1179", status: "blocked" },
+      { identifier: "PAP-1180", status: "done" },
+    ]);
+
+    expect(html).toContain('href="/issues/PAP-1179"');
+    expect(html).toContain('href="/issues/PAP-1180"');
+    expect(html).toContain(">/issues/PAP-1179<");
+    expect(html).toContain(">/PAP/issues/pap-1180<");
+    expect(html).toContain("text-red-600");
+    expect(html).toContain("text-green-600");
+  });
+
+  it("does not auto-link non-issue internal route paths", () => {
+    const html = renderMarkdown("Use /issues/new for the creation form, /issues/PAP-42extra as text, and /api/issues for data.");
+
+    expect(html).toContain("Use /issues/new for the creation form, /issues/PAP-42extra as text, and /api/issues for data.");
+    expect(html).not.toContain('href="/issues/new"');
+    expect(html).not.toContain('href="/issues/PAP-42"');
+    expect(html).not.toContain('data-mention-kind="issue"');
+  });
+
   it("rewrites issue scheme links to internal issue links", () => {
     const html = renderMarkdown("See issue://PAP-1310 and issue://:PAP-1311.", [
       { identifier: "PAP-1310", status: "done" },
@@ -192,6 +230,22 @@ describe("MarkdownBody", () => {
     expect(html).toContain('href="/issues/PAP-1271"');
     expect(html).toContain('<code style="overflow-wrap:anywhere;word-break:break-word">PAP-1271</code>');
     expect(html).toContain("text-green-600");
+    expect(html).toContain("paperclip-markdown-issue-ref");
+  });
+
+  it("keeps trailing punctuation outside auto-linked issue references", () => {
+    const html = renderMarkdown("See PAP-1271: /issues/PAP-1272] and issue://PAP-1273.", [
+      { identifier: "PAP-1271", status: "done" },
+      { identifier: "PAP-1272", status: "blocked" },
+      { identifier: "PAP-1273", status: "todo" },
+    ]);
+
+    expect(html).toContain('<a href="/issues/PAP-1271"');
+    expect(html).toContain('>PAP-1271</a>:');
+    expect(html).toContain('<a href="/issues/PAP-1272"');
+    expect(html).toContain('>/issues/PAP-1272</a>]');
+    expect(html).toContain('<a href="/issues/PAP-1273"');
+    expect(html).toContain('>issue://PAP-1273</a>.');
   });
 
   it("can opt out of issue reference linkification for offline previews", () => {
@@ -277,7 +331,7 @@ describe("MarkdownBody", () => {
     expect(html).toContain('style="max-width:100%;overflow-x:auto"');
   });
 
-  it("renders internal issue links and bare identifiers as issue chips", () => {
+  it("renders internal issue links and bare identifiers as inline issue refs", () => {
     const html = renderMarkdown(`See PAP-42 and [linked task](${buildIssueReferenceHref("PAP-77")}) for follow-up.`, [
       { identifier: "PAP-42", status: "done" },
       { identifier: "PAP-77", status: "blocked" },
@@ -286,5 +340,7 @@ describe("MarkdownBody", () => {
     expect(html).toContain('href="/issues/PAP-42"');
     expect(html).toContain('href="/issues/PAP-77"');
     expect(html).toContain('data-mention-kind="issue"');
+    expect(html).toContain("paperclip-markdown-issue-ref");
+    expect(html).not.toContain("paperclip-mention-chip--issue");
   });
 });

ui/src/components/MarkdownBody.tsx

@@ -4,11 +4,11 @@ import { Github } from "lucide-react";
 import Markdown, { defaultUrlTransform, type Components, type Options } from "react-markdown";
 import remarkGfm from "remark-gfm";
 import { cn } from "../lib/utils";
+import { Link } from "@/lib/router";
 import { useTheme } from "../context/ThemeContext";
 import { mentionChipInlineStyle, parseMentionChipHref } from "../lib/mention-chips";
 import { issuesApi } from "../api/issues";
 import { queryKeys } from "../lib/queryKeys";
-import { Link } from "@/lib/router";
 import { parseIssueReferenceFromHref, remarkLinkIssueReferences } from "../lib/issue-reference";
 import { remarkSoftBreaks } from "../lib/remark-soft-breaks";
 import { StatusIcon } from "./StatusIcon";
@@ -29,11 +29,9 @@ let mermaidLoaderPromise: Promise<typeof import("mermaid").default> | null = nul
 
 function MarkdownIssueLink({
   issuePathId,
-  href,
   children,
 }: {
   issuePathId: string;
-  href: string;
   children: ReactNode;
 }) {
   const { data } = useQuery({
@@ -42,14 +40,23 @@ function MarkdownIssueLink({
     staleTime: 60_000,
   });
 
+  const identifier = data?.identifier ?? issuePathId;
+  const title = data?.title ?? identifier;
+  const status = data?.status;
+  const issueLabel = title !== identifier ? `Issue ${identifier}: ${title}` : `Issue ${identifier}`;
+
   return (
     <Link
-      to={href}
+      to={`/issues/${identifier}`}
-      className="inline-flex items-center gap-1 align-baseline font-medium"
       data-mention-kind="issue"
+      className="paperclip-markdown-issue-ref"
+      title={title}
+      aria-label={issueLabel}
     >
-      {data ? <StatusIcon status={data.status} className="h-3.5 w-3.5" /> : null}
+      {status ? (
-      <span>{children}</span>
+        <StatusIcon status={status} className="mr-1 h-3 w-3 align-[-0.125em]" />
+      ) : null}
+      {children}
     </Link>
   );
 }
@@ -240,7 +247,7 @@ export function MarkdownBody({
       const issueRef = linkIssueReferences ? parseIssueReferenceFromHref(href) : null;
       if (issueRef) {
         return (
-          <MarkdownIssueLink issuePathId={issueRef.issuePathId} href={issueRef.href}>
+          <MarkdownIssueLink issuePathId={issueRef.issuePathId}>
             {linkChildren}
           </MarkdownIssueLink>
         );

ui/src/index.css

@@ -448,11 +448,23 @@
   font-size: 0.75rem;
   line-height: 1.3;
   text-decoration: none;
-  vertical-align: middle;
+  vertical-align: baseline;
   white-space: nowrap;
   user-select: none;
 }
 
+/* Strip the MDXEditor's default inline-code styling from the text inside chips
+   (the link label otherwise picks up a monospace font + gray tint). */
+.paperclip-mdxeditor-content a.paperclip-mention-chip,
+.paperclip-mdxeditor-content a.paperclip-mention-chip code,
+.paperclip-mdxeditor-content a.paperclip-project-mention-chip,
+.paperclip-mdxeditor-content a.paperclip-project-mention-chip code {
+  font-family: inherit;
+  background: none;
+  color: inherit;
+  padding: 0;
+}
+
 .paperclip-mdxeditor-content a.paperclip-mention-chip::before,
 a.paperclip-mention-chip::before {
   content: "";
@@ -768,6 +780,13 @@ a.paperclip-mention-chip[data-mention-kind="agent"]::before {
   background: color-mix(in oklab, var(--accent) 42%, transparent);
 }
 
+/* Inline issue references in markdown: no pill chrome, just a status icon
+   beside the link label — keeps the pair from splitting across lines. */
+.paperclip-markdown-issue-ref {
+  display: inline;
+  white-space: nowrap;
+}
+
 .dark .paperclip-markdown a {
   color: color-mix(in oklab, var(--foreground) 80%, #58a6ff 20%);
 }
@@ -832,9 +851,11 @@ a.paperclip-mention-chip[data-mention-kind="agent"]::before {
   background: transparent;
 }
 
-/* Project mention chips rendered inside MarkdownBody */
+/* Mention chips rendered inline in prose (MarkdownBody or inline anchors) */
 a.paperclip-mention-chip,
-a.paperclip-project-mention-chip {
+a.paperclip-project-mention-chip,
+span.paperclip-mention-chip,
+span.paperclip-project-mention-chip {
   display: inline-flex;
   align-items: center;
   gap: 0.25rem;
@@ -845,10 +866,25 @@ a.paperclip-project-mention-chip {
   font-size: 0.75rem;
   line-height: 1.3;
   text-decoration: none;
-  vertical-align: middle;
+  /* Align the pill relative to the surrounding text baseline instead of its
+     x-height midpoint so it sits on the text line rather than floating above. */
+  vertical-align: baseline;
   white-space: nowrap;
 }
 
+/* When the identifier inside a chip is backtick-wrapped in markdown, strip the
+   inline-code monospace/gray styling so the pill label reads cleanly. */
+.paperclip-markdown a.paperclip-mention-chip code,
+.paperclip-markdown a.paperclip-project-mention-chip code,
+.paperclip-markdown span.paperclip-mention-chip code,
+.paperclip-markdown span.paperclip-project-mention-chip code {
+  font-family: inherit;
+  background: none;
+  color: inherit;
+  padding: 0;
+  font-size: inherit;
+}
+
 /* Keep MDXEditor popups above app dialogs, even when they portal to <body>. */
 [class*="_popupContainer_"] {
   z-index: 81 !important;

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);
   }