Make thread store process-scoped (#19474)

- Build one app-server process ThreadStore from startup config and share
it with ThreadManager and CodexMessageProcessor.
- Remove per-thread/fork store reconstruction so effective thread config
cannot switch the persistence backend.
- Add params to ThreadStore create/resume for specifying thread
metadata, since otherwise the metadata from store creation would be used
(incorrectly).

codex-rs/core/tests/suite/code_mode.rs

@@ -2556,7 +2556,6 @@ async fn code_mode_can_call_hidden_dynamic_tools() -> Result<()> {
         .thread_manager
         .start_thread_with_tools(
             base_test.config.clone(),
-            codex_core::thread_store_from_config(&base_test.config),
             vec![DynamicToolSpec {
                 namespace: Some("codex_app".to_string()),
                 name: "hidden_dynamic_tool".to_string(),