[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/core/src/realtime_context_tests.rs

@@ -47,6 +47,10 @@ fn stored_thread(cwd: &str, title: &str, first_user_message: &str) -> StoredThre
             .timestamp_opt(1_709_251_200, 0)
             .single()
             .expect("valid timestamp"),
+        recency_at: Utc
+            .timestamp_opt(1_709_251_200, 0)
+            .single()
+            .expect("valid timestamp"),
         archived_at: None,
         cwd: PathBuf::from(cwd),
         cli_version: "test".to_string(),