[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/schema/json/v2/ThreadMetadataUpdateResponse.json

@@ -870,6 +870,14 @@
           "description": "Usually the first user message in the thread, if available.",
           "type": "string"
         },
+        "recencyAt": {
+          "description": "Unix timestamp (in seconds) used for thread recency ordering.",
+          "format": "int64",
+          "type": [
+            "integer",
+            "null"
+          ]
+        },
         "sessionId": {
           "description": "Session id shared by threads that belong to the same session tree.",
           "type": "string"