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/mcp-server/src/codex_tool_runner.rs

@@ -13,7 +13,6 @@ use codex_core::CodexThread;
 use codex_core::NewThread;
 use codex_core::ThreadManager;
 use codex_core::config::Config as CodexConfig;
-use codex_core::thread_store_from_config;
 use codex_protocol::ThreadId;
 use codex_protocol::protocol::AgentMessageEvent;
 use codex_protocol::protocol::ApplyPatchApprovalRequestEvent;
@@ -69,10 +68,7 @@ pub async fn run_codex_tool_session(
         thread_id,
         thread,
         session_configured,
-    } = match thread_manager
-        .start_thread(config.clone(), thread_store_from_config(&config))
-        .await
-    {
+    } = match thread_manager.start_thread(config.clone()).await {
         Ok(res) => res,
         Err(e) => {
             let result = CallToolResult {

codex-rs/mcp-server/src/message_processor.rs

@@ -4,6 +4,7 @@ use std::sync::Arc;
 use codex_arg0::Arg0DispatchPaths;
 use codex_core::ThreadManager;
 use codex_core::config::Config;
+use codex_core::thread_store_from_config;
 use codex_exec_server::EnvironmentManager;
 use codex_login::AuthManager;
 use codex_login::default_client::USER_AGENT_SUFFIX;
@@ -65,6 +66,7 @@ impl MessageProcessor {
             SessionSource::Mcp,
             environment_manager,
             /*analytics_events_client*/ None,
+            thread_store_from_config(config.as_ref()),
         ));
         Self {
             outgoing,