[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/src/bespoke_event_handling.rs

@@ -2261,6 +2261,7 @@ mod tests {
             reasoning_effort: None,
             created_at,
             updated_at: created_at,
+            recency_at: created_at,
             archived_at: None,
             cwd: test_path_buf("/tmp").abs().into(),
             cli_version: "0.0.0".to_string(),

codex-rs/app-server/src/request_processors/thread_processor.rs

@@ -1897,6 +1897,7 @@ impl ThreadRequestProcessor {
         let store_sort_key = match sort_key.unwrap_or(ThreadSortKey::CreatedAt) {
             ThreadSortKey::CreatedAt => StoreThreadSortKey::CreatedAt,
             ThreadSortKey::UpdatedAt => StoreThreadSortKey::UpdatedAt,
+            ThreadSortKey::RecencyAt => StoreThreadSortKey::RecencyAt,
         };
         let sort_direction = sort_direction.unwrap_or(SortDirection::Desc);
         let (stored_threads, next_cursor) = self
@@ -1978,6 +1979,7 @@ impl ThreadRequestProcessor {
         let store_sort_key = match sort_key.unwrap_or(ThreadSortKey::CreatedAt) {
             ThreadSortKey::CreatedAt => StoreThreadSortKey::CreatedAt,
             ThreadSortKey::UpdatedAt => StoreThreadSortKey::UpdatedAt,
+            ThreadSortKey::RecencyAt => StoreThreadSortKey::RecencyAt,
         };
         let store_sort_direction = sort_direction.unwrap_or(SortDirection::Desc);
         let (allowed_sources, source_kind_filter) = compute_source_filters(source_kinds);
@@ -3695,6 +3697,7 @@ fn thread_backwards_cursor_for_sort_key(
     let timestamp = match sort_key {
         StoreThreadSortKey::CreatedAt => thread.created_at,
         StoreThreadSortKey::UpdatedAt => thread.updated_at,
+        StoreThreadSortKey::RecencyAt => thread.recency_at,
     };
     // The state DB stores unique millisecond timestamps. Offset the reverse cursor by one
     // millisecond so the opposite-direction query includes the page anchor.
@@ -4139,6 +4142,7 @@ pub(crate) fn thread_from_stored_thread(
         },
         created_at: thread.created_at.timestamp(),
         updated_at: thread.updated_at.timestamp(),
+        recency_at: Some(thread.recency_at.timestamp()),
         status: ThreadStatus::NotLoaded,
         path,
         cwd,
@@ -4344,6 +4348,7 @@ fn build_thread_from_snapshot(
         model_provider: config_snapshot.model_provider_id.clone(),
         created_at: now,
         updated_at: now,
+        recency_at: Some(now),
         status: ThreadStatus::NotLoaded,
         path,
         cwd: config_snapshot.cwd().clone(),

codex-rs/app-server/src/request_processors/thread_processor_tests.rs

@@ -478,6 +478,7 @@ mod thread_processor_behavior_tests {
             reasoning_effort: None,
             created_at: created_at.with_timezone(&Utc),
             updated_at: updated_at.with_timezone(&Utc),
+            recency_at: updated_at.with_timezone(&Utc),
             archived_at: None,
             cwd: PathBuf::from("/tmp"),
             cli_version: "0.0.0".to_string(),

codex-rs/app-server/src/request_processors/thread_resume_redaction.rs

@@ -178,6 +178,7 @@ mod tests {
             model_provider: "mock_provider".to_string(),
             created_at: 0,
             updated_at: 0,
+            recency_at: Some(0),
             status: ThreadStatus::Idle,
             path: None,
             cwd: test_path_buf("/tmp").abs(),

codex-rs/app-server/src/request_processors/thread_summary.rs

@@ -320,6 +320,7 @@ pub(crate) fn summary_to_thread(
         model_provider,
         created_at: created_at.map(|dt| dt.timestamp()).unwrap_or(0),
         updated_at: updated_at.map(|dt| dt.timestamp()).unwrap_or(0),
+        recency_at: updated_at.map(|dt| dt.timestamp()),
         status: ThreadStatus::NotLoaded,
         path: (!path.as_os_str().is_empty()).then_some(path),
         cwd,

codex-rs/app-server/src/thread_status.rs

@@ -897,6 +897,7 @@ mod tests {
             model_provider: "mock-provider".to_string(),
             created_at: 0,
             updated_at: 0,
+            recency_at: Some(0),
             status: ThreadStatus::NotLoaded,
             path: None,
             cwd: test_path_buf("/tmp").abs(),