[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/state/src/migrations.rs

@@ -1,5 +1,6 @@
 use std::borrow::Cow;
 
+use sqlx::SqlitePool;
 use sqlx::migrate::Migrator;
 
 pub(crate) static STATE_MIGRATOR: Migrator = sqlx::migrate!("./migrations");
@@ -39,3 +40,49 @@ pub(crate) fn runtime_goals_migrator() -> Migrator {
 pub(crate) fn runtime_memories_migrator() -> Migrator {
     runtime_migrator(&MEMORIES_MIGRATOR)
 }
+
+pub(crate) async fn repair_legacy_recency_migration_version(
+    pool: &SqlitePool,
+    migrator: &Migrator,
+) -> anyhow::Result<()> {
+    let Some(recency_migration) = migrator
+        .migrations
+        .iter()
+        .find(|migration| migration.version == 39)
+    else {
+        return Ok(());
+    };
+    let migrations_table_exists = sqlx::query_scalar::<_, i64>(
+        "SELECT 1 FROM sqlite_master WHERE type = 'table' AND name = '_sqlx_migrations'",
+    )
+    .fetch_optional(pool)
+    .await?
+    .is_some();
+    if !migrations_table_exists {
+        return Ok(());
+    }
+
+    sqlx::query(
+        r#"
+UPDATE _sqlx_migrations
+SET version = ?, description = ?
+WHERE version = ?
+  AND checksum = ?
+  AND NOT EXISTS (
+      SELECT 1 FROM _sqlx_migrations WHERE version = ?
+  )
+        "#,
+    )
+    .bind(recency_migration.version)
+    .bind(recency_migration.description.as_ref())
+    .bind(38_i64)
+    .bind(recency_migration.checksum.as_ref())
+    .bind(recency_migration.version)
+    .execute(pool)
+    .await?;
+    Ok(())
+}
+
+#[cfg(test)]
+#[path = "migrations_tests.rs"]
+mod tests;