[codex] Polish issue board workflows (#4224)

## Thinking Path

> - Paperclip orchestrates AI agents for zero-human companies
> - Human operators supervise that work through issue lists, issue
detail, comments, inbox groups, markdown references, and
profile/activity surfaces
> - The branch had many small UI fixes that improve the operator loop
but do not need to ship with backend runtime migrations
> - These changes belong together as board workflow polish because they
affect scanning, navigation, issue context, comment state, and markdown
clarity
> - This pull request groups the UI-only slice so it can merge
independently from runtime/backend changes
> - The benefit is a clearer board experience with better issue context,
steadier optimistic updates, and more predictable keyboard navigation

## What Changed

- Improves issue properties, sub-issue actions, blocker chips, and issue
list/detail refresh behavior.
- Adds blocker context above the issue composer and stabilizes
queued/interrupted comment UI state.
- Improves markdown issue/GitHub link rendering and opens external
markdown links in a new tab.
- Adds inbox group keyboard navigation and fold/unfold support.
- Polishes activity/avatar/profile/settings/workspace presentation
details.

## Verification

- `pnpm exec vitest run ui/src/components/IssueProperties.test.tsx
ui/src/components/IssueChatThread.test.tsx
ui/src/components/MarkdownBody.test.tsx ui/src/lib/inbox.test.ts
ui/src/lib/optimistic-issue-comments.test.ts`

## Risks

- Low to medium risk: changes are UI-focused but cover high-traffic
issue and inbox surfaces.
- This branch intentionally does not include the backend runtime changes
from the companion PR; where UI calls newer API filters, unsupported
servers should continue to fail visibly through existing API error
handling.
- Visual screenshots were not captured in this heartbeat; targeted
component/helper tests cover the changed behavior.

> 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 runtime, shell/git tool use
enabled. Exact hosted model build and context window are not exposed in
this Paperclip heartbeat 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
- [x] 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

ui/src/context/LiveUpdatesProvider.test.ts

@@ -321,30 +321,32 @@ describe("LiveUpdatesProvider issue invalidation", () => {
 
   it("refreshes visible issue run queries when the displayed run changes status", () => {
     const invalidations: unknown[] = [];
+    const cache = new Map<string, unknown>([
+      [JSON.stringify(queryKeys.issues.detail("PAP-759")), {
+        id: "issue-1",
+        identifier: "PAP-759",
+        assigneeAgentId: "agent-1",
+        executionRunId: "run-1",
+        executionAgentNameKey: "codexcoder",
+        executionLockedAt: new Date("2026-04-08T21:00:00.000Z"),
+      }],
+      [JSON.stringify(queryKeys.issues.activeRun("PAP-759")), {
+        id: "run-1",
+      }],
+      [JSON.stringify(queryKeys.issues.liveRuns("PAP-759")), [{ id: "run-1" }]],
+      [JSON.stringify(queryKeys.issues.runs("PAP-759")), [{ runId: "run-1" }]],
+    ]);
     const queryClient = {
       invalidateQueries: (input: unknown) => {
         invalidations.push(input);
       },
       getQueryData: (key: unknown) => {
-        if (JSON.stringify(key) === JSON.stringify(queryKeys.issues.detail("PAP-759"))) {
-          return {
-            id: "issue-1",
-            identifier: "PAP-759",
-            assigneeAgentId: "agent-1",
-          };
-        }
-        if (JSON.stringify(key) === JSON.stringify(queryKeys.issues.activeRun("PAP-759"))) {
-          return {
-            id: "run-1",
-          };
-        }
-        if (JSON.stringify(key) === JSON.stringify(queryKeys.issues.liveRuns("PAP-759"))) {
-          return [{ id: "run-1" }];
-        }
-        if (JSON.stringify(key) === JSON.stringify(queryKeys.issues.runs("PAP-759"))) {
-          return [{ runId: "run-1" }];
-        }
-        return undefined;
+        return cache.get(JSON.stringify(key));
+      },
+      setQueryData: (key: unknown, updater: unknown) => {
+        const cacheKey = JSON.stringify(key);
+        const current = cache.get(cacheKey);
+        cache.set(cacheKey, typeof updater === "function" ? updater(current) : updater);
       },
     };
 
@@ -375,6 +377,13 @@ describe("LiveUpdatesProvider issue invalidation", () => {
     expect(invalidations).toContainEqual({
       queryKey: queryKeys.issues.activeRun("PAP-759"),
     });
+    expect(cache.get(JSON.stringify(queryKeys.issues.activeRun("PAP-759")))).toBeNull();
+    expect(cache.get(JSON.stringify(queryKeys.issues.liveRuns("PAP-759")))).toEqual([]);
+    expect(cache.get(JSON.stringify(queryKeys.issues.detail("PAP-759")))).toMatchObject({
+      executionRunId: null,
+      executionAgentNameKey: null,
+      executionLockedAt: null,
+    });
   });
 
   it("ignores run status events for other issues", () => {
@@ -404,6 +413,7 @@ describe("LiveUpdatesProvider issue invalidation", () => {
         }
         return undefined;
       },
+      setQueryData: vi.fn(),
     };
 
     const invalidated = __liveUpdatesTestUtils.invalidateVisibleIssueRunQueries(

ui/src/context/LiveUpdatesProvider.tsx

@@ -10,6 +10,7 @@ import { useCompany } from "./CompanyContext";
 import type { ToastInput } from "./ToastContext";
 import { useToastActions } from "./ToastContext";
 import { upsertIssueCommentInPages } from "../lib/optimistic-issue-comments";
+import { clearIssueExecutionRun, removeLiveRunById } from "../lib/optimistic-issue-runs";
 import { queryKeys } from "../lib/queryKeys";
 import { toCompanyRelativePath } from "../lib/company-routes";
 import { useLocation } from "../lib/router";
@@ -19,6 +20,7 @@ const TOAST_COOLDOWN_MAX = 3;
 const RECONNECT_SUPPRESS_MS = 2000;
 const SOCKET_CONNECTING = 0;
 const SOCKET_OPEN = 1;
+const TERMINAL_RUN_STATUSES = new Set(["succeeded", "failed", "cancelled", "timed_out"]);
 
 type LiveUpdatesSocketLike = {
   readyState: number;
@@ -275,6 +277,22 @@ function invalidateVisibleIssueRunQueries(
     (!!agentId && !!context.assigneeAgentId && agentId === context.assigneeAgentId);
   if (!matchesVisibleIssue) return false;
 
+  const status = readString(payload.status);
+  if (runId && status && TERMINAL_RUN_STATUSES.has(status)) {
+    queryClient.setQueryData(
+      queryKeys.issues.liveRuns(context.routeIssueRef),
+      (current: LiveRunForIssue[] | undefined) => removeLiveRunById(current, runId),
+    );
+    queryClient.setQueryData(
+      queryKeys.issues.activeRun(context.routeIssueRef),
+      (current: ActiveRunForIssue | null | undefined) => (current?.id === runId ? null : current),
+    );
+    queryClient.setQueryData(
+      queryKeys.issues.detail(context.routeIssueRef),
+      (current: Issue | undefined) => clearIssueExecutionRun(current, runId),
+    );
+  }
+
   queryClient.invalidateQueries({ queryKey: queryKeys.issues.detail(context.routeIssueRef) });
   queryClient.invalidateQueries({ queryKey: queryKeys.issues.activity(context.routeIssueRef) });
   queryClient.invalidateQueries({ queryKey: queryKeys.issues.runs(context.routeIssueRef) });