thread-store: store permission profiles (#23165)

## Why

`SandboxPolicy` is the legacy compatibility shape, but
`codex-thread-store` still exposed it through `StoredThread`,
`ThreadMetadataPatch`, and live metadata sync. That kept thread-store
consumers tied to the legacy representation and meant richer permission
profile data could not round-trip through thread metadata or cold
rollout reconciliation.

## What Changed

- Replaced thread-store `sandbox_policy` API fields with canonical
`PermissionProfile` fields.
- Persist new permission-profile metadata as canonical JSON in the
existing SQLite metadata slot while continuing to read older legacy
sandbox policy values.
- Updated local, in-memory, live metadata sync, and rollout extraction
paths to propagate `TurnContextItem::permission_profile()`.
- Re-materialize legacy permission metadata against the final rollout
cwd when rollout-derived metadata replaces stale SQLite summaries.
- Updated affected app-server and core test constructors to build
`PermissionProfile` values directly.

## Test Plan

- `cargo test -p codex-state`
- `cargo test -p codex-thread-store`
- `cargo test -p codex-app-server
summary_from_stored_thread_preserves_millisecond_precision --lib`
- `cargo test -p codex-core realtime_context --lib`

codex-rs/core/src/realtime_context_tests.rs

@@ -13,10 +13,10 @@ use chrono::Utc;
 use codex_git_utils::GitSha;
 use codex_protocol::ThreadId;
 use codex_protocol::models::ContentItem;
+use codex_protocol::models::PermissionProfile;
 use codex_protocol::models::ResponseItem;
 use codex_protocol::protocol::AskForApproval;
 use codex_protocol::protocol::GitInfo;
-use codex_protocol::protocol::SandboxPolicy;
 use codex_protocol::protocol::SessionSource;
 use codex_thread_store::StoredThread;
 use core_test_support::PathBufExt;
@@ -59,7 +59,7 @@ fn stored_thread(cwd: &str, title: &str, first_user_message: &str) -> StoredThre
             repository_url: None,
         }),
         approval_mode: AskForApproval::Never,
-        sandbox_policy: SandboxPolicy::new_read_only_policy(),
+        permission_profile: PermissionProfile::read_only(),
         token_usage: None,
         first_user_message: Some(first_user_message.to_string()),
         history: None,