[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/rollout/src/tests.rs

@@ -612,6 +612,7 @@ async fn test_list_conversations_latest_first() {
                 model_provider: Some(TEST_PROVIDER.to_string()),
                 cli_version: Some("test_version".to_string()),
                 created_at: Some("2025-01-03T12-00-00".into()),
+                recency_at: updated_times.first().cloned().flatten(),
                 updated_at: updated_times.first().cloned().flatten(),
             },
             ThreadItem {
@@ -630,6 +631,7 @@ async fn test_list_conversations_latest_first() {
                 model_provider: Some(TEST_PROVIDER.to_string()),
                 cli_version: Some("test_version".to_string()),
                 created_at: Some("2025-01-02T12-00-00".into()),
+                recency_at: updated_times.get(1).cloned().flatten(),
                 updated_at: updated_times.get(1).cloned().flatten(),
             },
             ThreadItem {
@@ -648,6 +650,7 @@ async fn test_list_conversations_latest_first() {
                 model_provider: Some(TEST_PROVIDER.to_string()),
                 cli_version: Some("test_version".to_string()),
                 created_at: Some("2025-01-01T12-00-00".into()),
+                recency_at: updated_times.get(2).cloned().flatten(),
                 updated_at: updated_times.get(2).cloned().flatten(),
             },
         ],
@@ -759,6 +762,7 @@ async fn test_pagination_cursor() {
                 model_provider: Some(TEST_PROVIDER.to_string()),
                 cli_version: Some("test_version".to_string()),
                 created_at: Some("2025-03-05T09-00-00".into()),
+                recency_at: updated_page1.first().cloned().flatten(),
                 updated_at: updated_page1.first().cloned().flatten(),
             },
             ThreadItem {
@@ -777,6 +781,7 @@ async fn test_pagination_cursor() {
                 model_provider: Some(TEST_PROVIDER.to_string()),
                 cli_version: Some("test_version".to_string()),
                 created_at: Some("2025-03-04T09-00-00".into()),
+                recency_at: updated_page1.get(1).cloned().flatten(),
                 updated_at: updated_page1.get(1).cloned().flatten(),
             },
         ],
@@ -831,6 +836,7 @@ async fn test_pagination_cursor() {
                 model_provider: Some(TEST_PROVIDER.to_string()),
                 cli_version: Some("test_version".to_string()),
                 created_at: Some("2025-03-03T09-00-00".into()),
+                recency_at: updated_page2.first().cloned().flatten(),
                 updated_at: updated_page2.first().cloned().flatten(),
             },
             ThreadItem {
@@ -849,6 +855,7 @@ async fn test_pagination_cursor() {
                 model_provider: Some(TEST_PROVIDER.to_string()),
                 cli_version: Some("test_version".to_string()),
                 created_at: Some("2025-03-02T09-00-00".into()),
+                recency_at: updated_page2.get(1).cloned().flatten(),
                 updated_at: updated_page2.get(1).cloned().flatten(),
             },
         ],
@@ -895,6 +902,7 @@ async fn test_pagination_cursor() {
             model_provider: Some(TEST_PROVIDER.to_string()),
             cli_version: Some("test_version".to_string()),
             created_at: Some("2025-03-01T09-00-00".into()),
+            recency_at: updated_page3.first().cloned().flatten(),
             updated_at: updated_page3.first().cloned().flatten(),
         }],
         next_cursor: None,
@@ -1066,6 +1074,7 @@ async fn test_get_thread_contents() {
             model_provider: Some(TEST_PROVIDER.to_string()),
             cli_version: Some("test_version".to_string()),
             created_at: Some(ts.into()),
+            recency_at: page.items[0].updated_at.clone(),
             updated_at: page.items[0].updated_at.clone(),
         }],
         next_cursor: None,
@@ -1421,6 +1430,7 @@ async fn test_timestamp_only_cursor_skips_same_second_filesystem_ties() {
                 model_provider: Some(TEST_PROVIDER.to_string()),
                 cli_version: Some("test_version".to_string()),
                 created_at: Some(ts.to_string()),
+                recency_at: updated_page1.first().cloned().flatten(),
                 updated_at: updated_page1.first().cloned().flatten(),
             },
             ThreadItem {
@@ -1439,6 +1449,7 @@ async fn test_timestamp_only_cursor_skips_same_second_filesystem_ties() {
                 model_provider: Some(TEST_PROVIDER.to_string()),
                 cli_version: Some("test_version".to_string()),
                 created_at: Some(ts.to_string()),
+                recency_at: updated_page1.get(1).cloned().flatten(),
                 updated_at: updated_page1.get(1).cloned().flatten(),
             },
         ],