[codex] Improve issue detail and issue-list UX (#3678)

## Thinking Path

> - Paperclip orchestrates AI agents for zero-human companies
> - A core part of that is the operator experience around reading issue
state, agent chat, and sub-task structure
> - The current branch had a long run of issue-detail and issue-list UX
fixes that all improve how humans follow and steer active work
> - Those changes mostly live in the UI/chat surface and should be
reviewed together instead of mixed with workspace/runtime work
> - This pull request packages the issue-detail, chat, markdown, and
sub-issue list improvements into one standalone change
> - The benefit is a cleaner, less jumpy, more reliable issue workflow
on desktop and mobile without coupling it to unrelated server/runtime
refactors

## What Changed

- Stabilized issue chat runtime wiring, optimistic comment handling,
queued-comment cancellation, and composer anchoring during live updates
- Fixed several issue-detail rendering and navigation regressions
including placeholder bleed, local polling scope, mobile inbox-to-issue
transitions, and visible refresh resets
- Improved markdown and rich-content handling with advisory image
normalization, editor fallback behavior, touch mention recovery, and
`issue:` quicklook links
- Refined sub-issue behavior with parent-derived defaults, current-user
inheritance fixes, empty-state cleanup, and a reusable issue-list
presentation for sub-issues
- Added targeted UI tests for the new issue-detail, chat scroll/message,
placeholder-data, markdown, and issue-list behaviors

## Verification

- `pnpm vitest run ui/src/components/IssueChatThread.test.tsx
ui/src/components/MarkdownEditor.test.tsx
ui/src/components/IssuesList.test.tsx
ui/src/context/LiveUpdatesProvider.test.tsx
ui/src/lib/issue-chat-messages.test.ts
ui/src/lib/issue-chat-scroll.test.ts
ui/src/lib/issue-detail-subissues.test.ts
ui/src/lib/query-placeholder-data.test.tsx
ui/src/hooks/usePaperclipIssueRuntime.test.tsx`

## Risks

- Medium: this branch touches the highest-traffic issue-detail UI paths,
so regressions would show up as chat/thread or sub-issue UX glitches
- The changes are UI-heavy and would benefit from reviewer screenshots
or a quick manual browser pass before merge

## Model Used

- OpenAI Codex coding agent (GPT-5-class runtime in Codex CLI; exact
deployed model ID is not exposed in this environment), reasoning
enabled, tool use and local code execution enabled

## 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 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.ts

@@ -6,7 +6,8 @@ type MarkdownNode = {
 };
 
 const BARE_ISSUE_IDENTIFIER_RE = /^[A-Z][A-Z0-9]+-\d+$/i;
-const ISSUE_REFERENCE_TOKEN_RE = /https?:\/\/[^\s<>()]+|\b[A-Z][A-Z0-9]+-\d+\b/gi;
+const ISSUE_SCHEME_RE = /^issue:\/\/:?([^?#\s]+)(?:[?#].*)?$/i;
+const ISSUE_REFERENCE_TOKEN_RE = /issue:\/\/:?[^\s<>()]+|https?:\/\/[^\s<>()]+|\b[A-Z][A-Z0-9]+-\d+\b/gi;
 
 export function parseIssuePathIdFromPath(pathOrUrl: string | null | undefined): string | null {
   if (!pathOrUrl) return null;
@@ -29,6 +30,16 @@ export function parseIssuePathIdFromPath(pathOrUrl: string | null | undefined):
 
 export function parseIssueReferenceFromHref(href: string | null | undefined) {
   if (!href) return null;
+  const trimmed = href.trim();
+  const issueSchemeMatch = trimmed.match(ISSUE_SCHEME_RE);
+  if (issueSchemeMatch?.[1]) {
+    const issuePathId = decodeURIComponent(issueSchemeMatch[1]);
+    return {
+      issuePathId,
+      href: `/issues/${encodeURIComponent(issuePathId)}`,
+    };
+  }
+
   const pathId = parseIssuePathIdFromPath(href);
   if (pathId) {
     return {
@@ -37,7 +48,6 @@ export function parseIssueReferenceFromHref(href: string | null | undefined) {
     };
   }
 
-  const trimmed = href.trim();
   if (!BARE_ISSUE_IDENTIFIER_RE.test(trimmed)) return null;
   const normalized = trimmed.toUpperCase();
   return {