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-protocol/src/protocol/v2.rs

@@ -2068,6 +2068,61 @@ pub struct ThreadUnarchiveParams {
 #[ts(export_to = "v2/")]
 pub struct ThreadSetNameResponse {}
 
+#[derive(Serialize, Deserialize, Debug, Clone, PartialEq, JsonSchema, TS)]
+#[serde(rename_all = "camelCase")]
+#[ts(export_to = "v2/")]
+pub struct ThreadMetadataUpdateParams {
+    pub thread_id: String,
+    /// Patch the stored Git metadata for this thread.
+    /// Omit a field to leave it unchanged, set it to `null` to clear it, or
+    /// provide a string to replace the stored value.
+    #[ts(optional = nullable)]
+    pub git_info: Option<ThreadMetadataGitInfoUpdateParams>,
+}
+
+#[derive(Serialize, Deserialize, Debug, Clone, PartialEq, JsonSchema, TS)]
+#[serde(rename_all = "camelCase")]
+#[ts(export_to = "v2/")]
+pub struct ThreadMetadataGitInfoUpdateParams {
+    /// Omit to leave the stored commit unchanged, set to `null` to clear it,
+    /// or provide a non-empty string to replace it.
+    #[serde(
+        default,
+        skip_serializing_if = "Option::is_none",
+        serialize_with = "super::serde_helpers::serialize_double_option",
+        deserialize_with = "super::serde_helpers::deserialize_double_option"
+    )]
+    #[ts(optional = nullable, type = "string | null")]
+    pub sha: Option<Option<String>>,
+    /// Omit to leave the stored branch unchanged, set to `null` to clear it,
+    /// or provide a non-empty string to replace it.
+    #[serde(
+        default,
+        skip_serializing_if = "Option::is_none",
+        serialize_with = "super::serde_helpers::serialize_double_option",
+        deserialize_with = "super::serde_helpers::deserialize_double_option"
+    )]
+    #[ts(optional = nullable, type = "string | null")]
+    pub branch: Option<Option<String>>,
+    /// Omit to leave the stored origin URL unchanged, set to `null` to clear it,
+    /// or provide a non-empty string to replace it.
+    #[serde(
+        default,
+        skip_serializing_if = "Option::is_none",
+        serialize_with = "super::serde_helpers::serialize_double_option",
+        deserialize_with = "super::serde_helpers::deserialize_double_option"
+    )]
+    #[ts(optional = nullable, type = "string | null")]
+    pub origin_url: Option<Option<String>>,
+}
+
+#[derive(Serialize, Deserialize, Debug, Clone, PartialEq, JsonSchema, TS)]
+#[serde(rename_all = "camelCase")]
+#[ts(export_to = "v2/")]
+pub struct ThreadMetadataUpdateResponse {
+    pub thread: Thread,
+}
+
 #[derive(Serialize, Deserialize, Debug, Clone, PartialEq, JsonSchema, TS)]
 #[serde(rename_all = "camelCase")]
 #[ts(export_to = "v2/")]