[codex] Restore thread recency with compatible migration history (#28671)

## Summary

- Revert #28655, restoring the thread `recencyAt` behavior introduced by
#27910.
- Move `threads_recency_at` to migration 0039 so it no longer collides
with `external_agent_config_imports` at version 0038.
- Repair databases that already applied the recency migration as version
38 by moving the matching migration-history row to version 39 before
SQLx validation. The current version-38 migration can then apply
normally.

## Validation

- `just test -p codex-state
migrations::tests::repairs_recency_migration_that_was_applied_as_version_38`
- `just test -p codex-state -p codex-rollout -p codex-thread-store -p
codex-app-server-protocol -p codex-tui`: 3,439 passed; six TUI tests
could not open the machine's existing read-only incident database at
`~/.codex/sqlite/state_5.sqlite`.
- `just fix -p codex-state`
- `just fmt`
- Verified that state migration versions are unique.

codex-rs/app-server-protocol/src/protocol/v2/thread_data.rs

@@ -152,6 +152,9 @@ pub struct Thread {
     /// Unix timestamp (in seconds) when the thread was last updated.
     #[ts(type = "number")]
     pub updated_at: i64,
+    /// Unix timestamp (in seconds) used for thread recency ordering.
+    #[ts(type = "number | null")]
+    pub recency_at: Option<i64>,
     /// Current runtime status for the thread.
     pub status: ThreadStatus,
     /// [UNSTABLE] Path to the thread on disk.