Revert state DB injection and agent graph store (#21481)

## Why

Reverts #20689 to restore the previous optional state DB plumbing. The
conflict resolution keeps the newer installation ID and session/thread
identity changes that landed after #20689, while removing the mandatory
state DB and agent graph store dependency from ThreadManager
construction.

## What changed

- Restored `Option<StateDbHandle>` through app-server, MCP server,
prompt debug, and test entry points.
- Removed the `codex-core` dependency on `codex-agent-graph-store` and
reverted descendant lookup back to the existing state DB path when
available.
- Kept newer `installation_id` forwarding by passing it beside the
optional DB handle.
- Kept local thread-name updates working when the optional state DB
handle is absent.

## Validation

- `git diff --check`
- `cargo test -p codex-thread-store`
- `cargo test -p codex-state -p codex-rollout -p
codex-app-server-protocol`
- Attempted `env CARGO_INCREMENTAL=0 cargo test -p codex-core -p
codex-app-server -p codex-app-server-client -p codex-mcp-server -p
codex-thread-manager-sample -p codex-tui`; blocked locally by a rustc
ICE while compiling `v8 v146.4.0` with `rustc 1.93.0 (254b59607
2026-01-19)` on `aarch64-apple-darwin`.

codex-rs/app-server-protocol/src/protocol/common.rs

@@ -1674,7 +1674,10 @@ mod tests {
 
         let plugin_list = ClientRequest::PluginList {
             request_id: request_id(),
-            params: v2::PluginListParams { cwds: None },
+            params: v2::PluginListParams {
+                cwds: None,
+                marketplace_kinds: None,
+            },
         };
         assert_eq!(
             plugin_list.serialization_scope(),