Add thread metadata update endpoint to app server (#13280)

## Summary
- add the v2 `thread/metadata/update` API, including
protocol/schema/TypeScript exports and app-server docs
- patch stored thread `gitInfo` in sqlite without resuming the thread,
with validation plus support for explicit `null` clears
- repair missing sqlite thread rows from rollout data before patching,
and make those repairs safe by inserting only when absent and updating
only git columns so newer metadata is not clobbered
- keep sqlite authoritative for mutable thread git metadata by
preserving existing sqlite git fields during reconcile/backfill and only
using rollout `SessionMeta` git fields to fill gaps
- add regression coverage for the endpoint, repair paths, concurrent
sqlite writes, clearing git fields, and rollout/backfill reconciliation
- fix the login server shutdown race so cancelling before the waiter
starts still terminates `block_until_done()` correctly

## Testing
- `cargo test -p codex-state
apply_rollout_items_preserves_existing_git_branch_and_fills_missing_git_fields`
- `cargo test -p codex-state
update_thread_git_info_preserves_newer_non_git_metadata`
- `cargo test -p codex-core
backfill_sessions_preserves_existing_git_branch_and_fills_missing_git_fields`
- `cargo test -p codex-app-server thread_metadata_update`
- `cargo test`
- currently fails in existing `codex-core` grep-files tests with
`unsupported call: grep_files`:
    - `suite::grep_files::grep_files_tool_collects_matches`
    - `suite::grep_files::grep_files_tool_reports_empty_results`

codex-rs/app-server/README.md

@@ -126,6 +126,7 @@ Example with notification opt-out:
 - `thread/list` — page through stored rollouts; supports cursor-based pagination and optional `modelProviders`, `sourceKinds`, `archived`, `cwd`, and `searchTerm` filters. Each returned `thread` includes `status` (`ThreadStatus`), defaulting to `notLoaded` when the thread is not currently loaded.
 - `thread/loaded/list` — list the thread ids currently loaded in memory.
 - `thread/read` — read a stored thread by id without resuming it; optionally include turns via `includeTurns`. The returned `thread` includes `status` (`ThreadStatus`), defaulting to `notLoaded` when the thread is not currently loaded.
+- `thread/metadata/update` — patch stored thread metadata in sqlite; currently supports updating persisted `gitInfo` fields and returns the refreshed `thread`.
 - `thread/status/changed` — notification emitted when a loaded thread’s status changes (`threadId` + new `status`).
 - `thread/archive` — move a thread’s rollout file into the archived directory; returns `{}` on success and emits `thread/archived`.
 - `thread/unsubscribe` — unsubscribe this connection from thread turn/item events. If this was the last subscriber, the server shuts down and unloads the thread, then emits `thread/closed`.
@@ -324,6 +325,34 @@ Use `thread/read` to fetch a stored thread by id without resuming it. Pass `incl
 } }
 ```
 
+### Example: Update stored thread metadata
+
+Use `thread/metadata/update` to patch sqlite-backed metadata for a thread without resuming it. Today this supports persisted `gitInfo`; omitted fields are left unchanged, while explicit `null` clears a stored value.
+
+```json
+{ "method": "thread/metadata/update", "id": 24, "params": {
+    "threadId": "thr_123",
+    "gitInfo": { "branch": "feature/sidebar-pr" }
+} }
+{ "id": 24, "result": {
+    "thread": {
+        "id": "thr_123",
+        "gitInfo": { "sha": null, "branch": "feature/sidebar-pr", "originUrl": null }
+    }
+} }
+
+{ "method": "thread/metadata/update", "id": 25, "params": {
+    "threadId": "thr_123",
+    "gitInfo": { "branch": null }
+} }
+{ "id": 25, "result": {
+    "thread": {
+        "id": "thr_123",
+        "gitInfo": null
+    }
+} }
+```
+
 ### Example: Archive a thread
 
 Use `thread/archive` to move the persisted rollout (stored as a JSONL file on disk) into the archived sessions directory.