Inject state DB, agent graph store (#20689)

## Why

We want the agent graph store to be passed down the stack as a real
dependency, the same way we already treat the thread store.

This will let us inject the agent graph store as a real dependency and
support implementations other than the local SQLite-backed one. Right
now most code instantiates a state DB and an agent graph store
just-in-time. Ideally, we would not depend on the state DB directly but
only read through the higher-level interfaces.

This change makes the dependency boundaries explicit and moves state DB
initialization to process bootstrap instead of hiding it inside local
store implementations.

## What changed

- `ThreadManager` now requires a `StateDbHandle` and an
`AgentGraphStore` at construction time instead of treating them as
optional internals.
- The local store constructors no longer lazily initialize SQLite.
Callers now initialize the state DB once per process and use that shared
handle to build:
  - `LocalThreadStore`
  - `LocalAgentGraphStore`
- App bootstraps (`app-server`, `mcp-server`, `prompt_debug`, and the
thread-manager sample) now initialize the state DB up front and inject
the resulting handle down the stack.
- `app-server` now consistently uses its process-scoped state DB handle
instead of reopening SQLite or trying to recover it from loaded threads.
- Device-key storage now reuses the shared state DB handle instead of
maintaining its own lazy opener.
- The thread archive / descendant traversal paths now use the injected
`AgentGraphStore` instead of reaching through local
thread-store-specific state.

## Verification

- `cargo check -p codex-core -p codex-thread-store -p codex-app-server
-p codex-mcp-server -p codex-thread-manager-sample --tests`
- `cargo test -p codex-thread-store`
- `cargo test -p codex-core
thread_manager_accepts_separate_agent_graph_store_and_thread_store --
--nocapture`
- `cargo test -p codex-app-server
thread_archive_archives_spawned_descendants -- --nocapture`

codex-rs/Cargo.lock

@@ -2411,6 +2411,7 @@ dependencies = [
  "bm25",
  "chrono",
  "clap",
+ "codex-agent-graph-store",
  "codex-analytics",
  "codex-api",
  "codex-app-server-protocol",