codex: route metadata updates through ThreadStore (#20576)

- Route `thread/metadata/update` through
`ThreadStore::update_thread_metadata`.
- Add `LocalThreadStore` git metadata patch support for set, partial
update, and clear semantics.
- Add some unit tests for the new thread store code
- Remove a lot of dead code/tests!

codex-rs/core/src/codex_thread.rs

@@ -32,7 +32,9 @@ use codex_protocol::protocol::ThreadMemoryMode;
 use codex_protocol::protocol::TokenUsageInfo;
 use codex_protocol::protocol::W3cTraceContext;
 use codex_protocol::user_input::UserInput;
+use codex_thread_store::StoredThread;
 use codex_thread_store::StoredThreadHistory;
+use codex_thread_store::ThreadMetadataPatch;
 use codex_thread_store::ThreadStoreError;
 use codex_thread_store::ThreadStoreResult;
 use codex_utils_absolute_path::AbsolutePathBuf;
@@ -411,6 +413,21 @@ impl CodexThread {
         live_thread.load_history(include_archived).await
     }
 
+    pub async fn update_thread_metadata(
+        &self,
+        patch: ThreadMetadataPatch,
+        include_archived: bool,
+    ) -> ThreadStoreResult<StoredThread> {
+        let live_thread = self
+            .codex
+            .session
+            .live_thread_for_persistence("update thread metadata")
+            .map_err(|err| ThreadStoreError::Internal {
+                message: err.to_string(),
+            })?;
+        live_thread.update_metadata(patch, include_archived).await
+    }
+
     pub fn state_db(&self) -> Option<StateDbHandle> {
         self.codex.state_db()
     }