fix(cli): accept renumbered migration journal order (#11684)
## Thinking Path > - Paperclip is the open source app people use to manage AI agents for work > - Worktree provisioning clones a source database into an isolated workspace > - Source validation must accept a migration journal that matches a prefix of the checkout journal > - Long-lived instances can apply migrations in a different order after migration files are renumbered > - The validator compared application order with filename order and rejected a valid source > - This pull request compares the resolved migration names as a set and records the checkout-prefix revision > - The benefit is that valid renumbered migration histories can pass source validation without allowing divergent histories ## Linked Issues or Issue Description **What happened?** Worktree seed source validation compared applied migrations in database application order with available migration files in filename order. A current source with the same migration set failed with `Migration journal is not a prefix` after migration files were renumbered. **Expected behavior** Source validation must accept a source when its resolved applied migration set equals a prefix of the checkout migration files. It must still reject a source that contains a resolved migration outside that prefix. **Steps to reproduce** 1. Apply migrations before a migration-file renumber operation. 2. Update the checkout so the same migration files have a different filename order. 3. Run worktree seed source validation against the long-lived source. 4. Observe that positional comparison rejects the source even though the sets are equal. **Paperclip version or commit** The bug reproduces on the master-equivalent worktree-seeding implementation before this commit. **Deployment mode** Local dev with embedded PostgreSQL. ## What Changed - Compare resolved applied migration names with the expected checkout prefix as an order-independent set. - Derive the reported source revision from the checkout prefix instead of database application order. - Add unit and embedded-PostgreSQL regressions for shuffled application order, stale unresolved rows, lagging sources, and true divergence. ## Verification - `pnpm exec vitest run cli/src/__tests__/worktree.test.ts` — 54 tests passed. - `pnpm --filter paperclipai typecheck` — passed. - The focused suite includes the real embedded-PostgreSQL seed path. ## Risks - Low risk. The change is limited to source migration-prefix validation. - The validator still rejects missing or unknown resolved migrations. - Duplicate resolved names remain set-equivalent by design. Raw stale journal rows remain tolerated. - Existing documentation already specifies order-independent checkout-prefix behavior, so no documentation change is required. > For core feature work, check [`ROADMAP.md`](ROADMAP.md) first and discuss it in `#dev` before opening the PR. Feature PRs that overlap with planned core work may need to be redirected — check the roadmap first. See `CONTRIBUTING.md`. ## Model Used - OpenAI Codex, exact model ID `gpt-5.6-sol`. The Codex runtime manages the context window. The model used reasoning, shell tools, code execution, and test execution. ## Checklist - [x] I have included a thinking path that traces from project context to this change - [x] I have specified the model used (with version and capability details) - [x] I have checked ROADMAP.md and confirmed this PR does not duplicate planned core work - [x] I have searched GitHub for duplicate or related PRs and linked them above - [x] I have either (a) linked existing issues with `Fixes: #` / `Closes #` / `Refs #` OR (b) described the issue in-PR following the relevant issue template - [x] I have not referenced internal/instance-local Paperclip issues or links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip` URLs) - [x] My branch name describes the change (e.g. `docs/...`, `fix/...`) and contains no internal Paperclip ticket id or instance-derived details - [x] I have run tests locally and they pass - [x] I have added or updated tests where applicable - [x] I have updated relevant documentation to reflect my changes - [x] I have considered and documented any risks above - [x] All Paperclip CI gates are green - [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups - [x] I will address all Greptile and reviewer comments before requesting merge Co-authored-by: Paperclip <noreply@paperclip.ing>
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51a843e135
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@ -488,14 +488,34 @@ describe("worktree helpers", () => {
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expect(full.nullifyColumns).toEqual({});
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});
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it("rejects a source migration journal that is ahead of the code journal", () => {
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it("rejects a source migration journal that diverges from the code journal", () => {
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expect(() => resolveWorktreeSeedMigrationRevision({
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status: "upToDate",
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tableCount: 1,
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availableMigrations: ["0001_initial.sql", "0002_current.sql"],
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appliedMigrations: ["0001_initial.sql", "0002_current.sql"],
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appliedMigrations: ["0001_initial.sql", "0003_unknown.sql"],
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journalEntryCount: 3,
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}, "sourcePrefix")).toThrow("Migration journal is ahead of this Paperclip checkout");
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}, "sourcePrefix")).toThrow("Migration journal is not a prefix of this Paperclip checkout");
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});
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it("accepts a current source whose migration application order differs from filename order", () => {
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expect(resolveWorktreeSeedMigrationRevision({
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status: "upToDate",
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tableCount: 1,
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availableMigrations: [
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"0001_initial.sql",
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"0002_renumbered.sql",
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"0003_applied_earlier.sql",
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"0004_current.sql",
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],
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appliedMigrations: [
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"0001_initial.sql",
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"0003_applied_earlier.sql",
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"0002_renumbered.sql",
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"0004_current.sql",
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],
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journalEntryCount: 6,
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}, "upToDate")).toBe("0004_current.sql");
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});
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it("accepts a source migration journal that is multiple revisions behind", () => {
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@ -508,9 +528,9 @@ describe("worktree helpers", () => {
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"0003_pending.sql",
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"0004_pending.sql",
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],
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appliedMigrations: ["0001_initial.sql", "0002_applied.sql"],
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appliedMigrations: ["0002_applied.sql", "0001_initial.sql"],
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pendingMigrations: ["0003_pending.sql", "0004_pending.sql"],
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journalEntryCount: 2,
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journalEntryCount: 3,
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reason: "pending-migrations",
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}, "sourcePrefix")).toBe("0002_applied.sql");
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});
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@ -1244,7 +1264,7 @@ describe("worktree helpers", () => {
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});
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itEmbeddedPostgres(
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"seeds a source whose migration journal is behind the code journal",
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"seeds a lagging source whose migration application order differs from filename order",
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async () => {
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const tempRoot = fs.mkdtempSync(path.join(os.tmpdir(), "paperclip-worktree-auth-seed-"));
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const worktreeRoot = path.join(tempRoot, "PAP-999-auth-seed");
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@ -1264,7 +1284,30 @@ describe("worktree helpers", () => {
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DELETE FROM "drizzle"."__drizzle_migrations"
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WHERE "id" = (
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SELECT max("id") FROM "drizzle"."__drizzle_migrations"
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);
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WITH pair AS (
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SELECT
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array_agg("id" ORDER BY "id" DESC) AS ids,
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array_agg("hash" ORDER BY "id" DESC) AS hashes
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FROM (
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SELECT "id", "hash"
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FROM "drizzle"."__drizzle_migrations"
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ORDER BY "id" DESC
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LIMIT 2
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) latest
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)
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UPDATE "drizzle"."__drizzle_migrations" migrations
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SET "hash" = CASE
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WHEN migrations."id" = pair.ids[1] THEN pair.hashes[2]
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WHEN migrations."id" = pair.ids[2] THEN pair.hashes[1]
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ELSE migrations."hash"
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END
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FROM pair
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WHERE migrations."id" IN (pair.ids[1], pair.ids[2]);
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INSERT INTO "drizzle"."__drizzle_migrations" ("hash", "created_at")
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VALUES ('stale-unresolvable-migration-hash', 0)
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`);
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await sourceDbClient.$client.end({ timeout: 5 });
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const laggingMigrationState = await inspectMigrations(sourceDb.connectionString);
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@ -1273,7 +1316,18 @@ describe("worktree helpers", () => {
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throw new Error("Expected the source migration journal to lag the code journal");
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}
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expect(laggingMigrationState.pendingMigrations).toHaveLength(1);
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const sourceMigrationRevision = laggingMigrationState.appliedMigrations.at(-1);
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const expectedAppliedPrefix = laggingMigrationState.availableMigrations.slice(
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0,
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laggingMigrationState.appliedMigrations.length,
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);
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expect(laggingMigrationState.appliedMigrations).not.toEqual(expectedAppliedPrefix);
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expect([...laggingMigrationState.appliedMigrations].sort()).toEqual(
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[...expectedAppliedPrefix].sort(),
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);
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expect(laggingMigrationState.journalEntryCount).toBeGreaterThan(
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laggingMigrationState.appliedMigrations.length,
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);
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const sourceMigrationRevision = expectedAppliedPrefix.at(-1);
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expect(sourceMigrationRevision).toBeTruthy();
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fs.mkdirSync(path.dirname(sourceKeyPath), { recursive: true });
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@ -1416,20 +1416,14 @@ export function resolveWorktreeSeedMigrationRevision(
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migrationState: Awaited<ReturnType<typeof inspectMigrations>>,
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requirement: "sourcePrefix" | "upToDate",
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): string {
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if (migrationState.journalEntryCount > migrationState.availableMigrations.length) {
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throw new Error(
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`Migration journal is ahead of this Paperclip checkout (${migrationState.journalEntryCount} applied migration(s), ${migrationState.availableMigrations.length} available).`,
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);
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}
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const expectedAppliedPrefix = migrationState.availableMigrations.slice(
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0,
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migrationState.appliedMigrations.length,
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);
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const appliedMigrationNames = new Set(migrationState.appliedMigrations);
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if (
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migrationState.appliedMigrations.some(
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(migration, index) => migration !== expectedAppliedPrefix[index],
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)
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appliedMigrationNames.size !== expectedAppliedPrefix.length ||
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expectedAppliedPrefix.some((migration) => !appliedMigrationNames.has(migration))
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) {
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throw new Error("Migration journal is not a prefix of this Paperclip checkout's migration journal.");
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}
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@ -1440,7 +1434,7 @@ export function resolveWorktreeSeedMigrationRevision(
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);
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}
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const migrationRevision = migrationState.appliedMigrations.at(-1);
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const migrationRevision = expectedAppliedPrefix.at(-1);
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if (!migrationRevision) {
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throw new Error("Migration journal has no applied revision.");
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}
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