[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/thread-store/src/in_memory.rs

@@ -535,6 +535,9 @@ fn stored_thread_from_state(
         updated_at: metadata
             .and_then(|metadata| metadata.updated_at)
             .unwrap_or_else(Utc::now),
+        recency_at: metadata
+            .and_then(|metadata| metadata.advance_recency_at.or(metadata.updated_at))
+            .unwrap_or_else(Utc::now),
         archived_at: None,
         cwd: metadata
             .and_then(|metadata| metadata.cwd.clone())