test(FN-5115): complete Step 7 — stabilize migrations and verification

Fusion-Task-Id: FN-5115
Fusion-Task-Lineage: 5c3d9d42-9dcd-4ebb-ba10-8a4b14d541dd

packages/core/src/__tests__/db-migrate.test.ts

@@ -715,7 +715,7 @@ describe("schema migration", () => {
 
     const row = db.prepare("SELECT deletedAt FROM tasks WHERE id = 'FN-legacy'").get() as { deletedAt: string | null };
     expect(row.deletedAt).toBeNull();
-    expect(db.getSchemaVersion()).toBe(87);
+    expect(db.getSchemaVersion()).toBe(88);
 
     db.close();
   });
@@ -748,7 +748,7 @@ describe("schema migration", () => {
       { id: "WS-001", mode: "prompt", gateMode: "advisory" },
       { id: "WS-002", mode: "script", gateMode: "advisory" },
     ]);
-    expect(db.getSchemaVersion()).toBe(87);
+    expect(db.getSchemaVersion()).toBe(88);
 
     db.close();
   });
@@ -798,7 +798,7 @@ describe("schema migration", () => {
       reviewerContextRetryCount: 0,
       reviewerFallbackRetryCount: 0,
     });
-    expect(db.getSchemaVersion()).toBe(87);
+    expect(db.getSchemaVersion()).toBe(88);
 
     db.close();
   });
@@ -827,7 +827,7 @@ describe("schema migration", () => {
 
     const columns = db.prepare("PRAGMA table_info(milestones)").all() as Array<{ name: string }>;
     expect(columns.map((column) => column.name)).toContain("acceptanceCriteria");
-    expect(db.getSchemaVersion()).toBe(87);
+    expect(db.getSchemaVersion()).toBe(88);
 
     db.close();
   });
@@ -862,7 +862,7 @@ describe("schema migration", () => {
       { id: "WS-002", mode: "script", enabled: 1, gateMode: "advisory" },
       { id: "WS-003", mode: "prompt", enabled: 0, gateMode: "advisory" },
     ]);
-    expect(db.getSchemaVersion()).toBe(87);
+    expect(db.getSchemaVersion()).toBe(88);
 
     db.close();
   });

packages/core/src/__tests__/db-paused-done-backfill.test.ts

@@ -3,7 +3,6 @@ import { mkdtempSync, readFileSync } from "node:fs";
 import { rm } from "node:fs/promises";
 import { join } from "node:path";
 import { tmpdir } from "node:os";
-import Sqlite from "better-sqlite3";
 import { Database } from "../db.js";
 import { TaskStore } from "../store.js";
 
@@ -28,6 +27,9 @@ describe("done paused backfill", () => {
     const seedStore = new TaskStore(rootDir, globalDir);
     await seedStore.init();
     const task = await seedStore.createTask({ description: "drifted done paused task" });
+    await seedStore.moveTask(task.id, "todo");
+    await seedStore.moveTask(task.id, "in-progress");
+    await seedStore.moveTask(task.id, "in-review");
     await seedStore.moveTask(task.id, "done");
     await seedStore.updateTask(task.id, {
       paused: true,
@@ -38,9 +40,10 @@ describe("done paused backfill", () => {
     seedStore.close();
 
     const fusionDir = join(rootDir, ".fusion");
-    const sqlite = new Sqlite(join(fusionDir, "fusion.db"));
-    sqlite.prepare("UPDATE __meta SET value = '87' WHERE key = 'schemaVersion'").run();
-    sqlite.close();
+    const schemaDowngradeDb = new Database(fusionDir);
+    schemaDowngradeDb.init();
+    schemaDowngradeDb.prepare("UPDATE __meta SET value = '87' WHERE key = 'schemaVersion'").run();
+    schemaDowngradeDb.close();
 
     const migrationLog = vi.spyOn(console, "log").mockImplementation(() => {});
     const db = new Database(fusionDir);

packages/core/src/__tests__/db.test.ts

@@ -291,7 +291,7 @@ describe("Database", () => {
     });
 
     it("seeds schema version", () => {
-      expect(db.getSchemaVersion()).toBe(87);
+      expect(db.getSchemaVersion()).toBe(88);
     });
 
     it("includes tokenUsageCacheWriteTokens on freshly initialized tasks table", () => {
@@ -319,7 +319,7 @@ describe("Database", () => {
 
     it("is idempotent - calling init() twice does not fail", () => {
       expect(() => db.init()).not.toThrow();
-      expect(db.getSchemaVersion()).toBe(87);
+      expect(db.getSchemaVersion()).toBe(88);
     });
     it("does not overwrite existing config on re-init", () => {
       // Update the config
@@ -1384,7 +1384,7 @@ describe("schema migrations", () => {
     db.init();
 
     // Verify version bumped to 29 (includes v1→v2 through v26→v29)
-    expect(db.getSchemaVersion()).toBe(87);
+    expect(db.getSchemaVersion()).toBe(88);
 
     // Verify new columns exist and existing data is intact
     const cols = db.prepare("PRAGMA table_info(tasks)").all() as Array<{ name: string }>;
@@ -1409,11 +1409,11 @@ describe("schema migrations", () => {
     const db = new Database(fusionDir);
     db.init();
 
-    expect(db.getSchemaVersion()).toBe(87);
+    expect(db.getSchemaVersion()).toBe(88);
 
     // Re-init should not fail
     db.init();
-    expect(db.getSchemaVersion()).toBe(87);
+    expect(db.getSchemaVersion()).toBe(88);
 
     db.close();
   });
@@ -1448,7 +1448,7 @@ describe("schema migrations", () => {
 
     db.init();
 
-    expect(db.getSchemaVersion()).toBe(87);
+    expect(db.getSchemaVersion()).toBe(88);
 
     const cols = db.prepare("PRAGMA table_info(tasks)").all() as Array<{ name: string }>;
     expect(cols.map((col) => col.name)).toContain("priority");
@@ -1489,7 +1489,7 @@ describe("schema migrations", () => {
 
     db.init();
 
-    expect(db.getSchemaVersion()).toBe(87);
+    expect(db.getSchemaVersion()).toBe(88);
 
     const cols = db.prepare("PRAGMA table_info(tasks)").all() as Array<{ name: string }>;
     const colNames = cols.map((col) => col.name);
@@ -1561,7 +1561,7 @@ describe("schema migrations", () => {
 
     db.init();
 
-    expect(db.getSchemaVersion()).toBe(87);
+    expect(db.getSchemaVersion()).toBe(88);
 
     const cols = db.prepare("PRAGMA table_info(tasks)").all() as Array<{ name: string }>;
     const colNames = cols.map((col) => col.name);
@@ -1801,7 +1801,7 @@ describe("schema migrations", () => {
 
     db.init();
 
-    expect(db.getSchemaVersion()).toBe(87);
+    expect(db.getSchemaVersion()).toBe(88);
 
     const cols = db.prepare("PRAGMA table_info(chat_messages)").all() as Array<{ name: string }>;
     expect(cols.map((col) => col.name)).toContain("attachments");
@@ -1875,7 +1875,7 @@ describe("schema migrations", () => {
 
     db.init();
 
-    expect(db.getSchemaVersion()).toBe(87);
+    expect(db.getSchemaVersion()).toBe(88);
 
     const tables = db.prepare("SELECT name FROM sqlite_master WHERE type='table' AND name = 'agentRatings'").all() as Array<{ name: string }>;
     expect(tables).toEqual([{ name: "agentRatings" }]);
@@ -1899,7 +1899,7 @@ describe("schema migrations", () => {
 
     db.init();
 
-    expect(db.getSchemaVersion()).toBe(87);
+    expect(db.getSchemaVersion()).toBe(88);
 
     const tables = db.prepare("SELECT name FROM sqlite_master WHERE type='table' AND name = 'mission_events'").all() as Array<{ name: string }>;
     expect(tables).toEqual([{ name: "mission_events" }]);
@@ -2003,7 +2003,7 @@ describe("schema migrations", () => {
     db.init();
 
     // Verify version bumped to 29
-    expect(db.getSchemaVersion()).toBe(87);
+    expect(db.getSchemaVersion()).toBe(88);
 
     // Verify new columns exist and existing data is intact
     const cols = db.prepare("PRAGMA table_info(tasks)").all() as Array<{ name: string }>;
@@ -2222,7 +2222,7 @@ describe("schema migrations", () => {
 
     localDb.init();
 
-    expect(localDb.getSchemaVersion()).toBe(87);
+    expect(localDb.getSchemaVersion()).toBe(88);
     const columns = localDb.prepare("PRAGMA table_info(tasks)").all() as Array<{ name: string }>;
     expect(columns.map((column) => column.name)).toContain("tokenUsageCacheWriteTokens");
 
@@ -2533,7 +2533,7 @@ describe("createDatabase factory", () => {
     const db = createDatabase(fusionDir);
     db.init();
 
-    expect(db.getSchemaVersion()).toBe(87);
+    expect(db.getSchemaVersion()).toBe(88);
     expect(db.getLastModified()).toBeGreaterThan(0);
 
     db.close();
@@ -2687,7 +2687,7 @@ describe("migration v77 task token budget columns", () => {
 
       migrated = new Database(fusion);
       migrated.init();
-      expect(migrated.getSchemaVersion()).toBe(87);
+      expect(migrated.getSchemaVersion()).toBe(88);
       const rows = migrated.prepare("PRAGMA table_info(tasks)").all() as Array<{ name: string }>;
       const names = new Set(rows.map((row) => row.name));
       expect(names.has("tokenBudgetSoftAlertedAt")).toBe(true);
@@ -2733,7 +2733,7 @@ describe("migration v67 drops orphan project auth tables", () => {
 
       migrated = new Database(fusion);
       migrated.init();
-      expect(migrated.getSchemaVersion()).toBe(87);
+      expect(migrated.getSchemaVersion()).toBe(88);
       const tables = migrated
         .prepare("SELECT name FROM sqlite_master WHERE type='table' AND name LIKE 'project_auth_%'")
         .all() as Array<{ name: string }>;
@@ -2760,7 +2760,7 @@ describe("migration v67 drops orphan project auth tables", () => {
 
     try {
       fresh.init();
-      expect(fresh.getSchemaVersion()).toBe(87);
+      expect(fresh.getSchemaVersion()).toBe(88);
       const tables = fresh
         .prepare("SELECT name FROM sqlite_master WHERE type='table' AND name LIKE 'project_auth_%'")
         .all() as Array<{ name: string }>;

packages/core/src/__tests__/insight-store.test.ts

@@ -1000,7 +1000,7 @@ describe("Migration: pre-33 DB upgrade", () => {
       // Step 1: Create a fresh database at v33 (runs all migrations up to 33)
       const db1 = createDatabase(legacyDir);
       db1.init();
-      expect(db1.getSchemaVersion()).toBe(87);
+      expect(db1.getSchemaVersion()).toBe(88);
       db1.close();
 
       // Step 2: Manually downgrade to version 32 and drop insight tables
@@ -1035,7 +1035,7 @@ describe("Migration: pre-33 DB upgrade", () => {
       expect(tableNamesBefore).not.toContain("project_insight_runs");
       // Now run init — this triggers the v32→v33 migration
       db3.init();
-      expect(db3.getSchemaVersion()).toBe(87);
+      expect(db3.getSchemaVersion()).toBe(88);
 
       // Step 4: Verify insight tables exist after migration
       const tablesAfter = db3.prepare(
@@ -1066,12 +1066,12 @@ describe("Migration: pre-33 DB upgrade", () => {
     try {
       const db1 = createDatabase(testDir);
       db1.init();
-      expect(db1.getSchemaVersion()).toBe(87);
+      expect(db1.getSchemaVersion()).toBe(88);
       db1.close();
 
       const db2 = createDatabase(testDir);
       expect(() => db2.init()).not.toThrow();
-      expect(db2.getSchemaVersion()).toBe(87);
+      expect(db2.getSchemaVersion()).toBe(88);
       db2.close();
     } finally {
       rmSync(testDir, { recursive: true, force: true });
@@ -1085,7 +1085,7 @@ describe("Migration: pre-33 DB upgrade", () => {
       // Step 1: Create a fresh DB and run migrations
       const db1 = createDatabase(compatDir);
       db1.init();
-      expect(db1.getSchemaVersion()).toBe(87);
+      expect(db1.getSchemaVersion()).toBe(88);
 
       // Step 2: Strip lifecycle and cancelledAt columns by recreating the
       // table without them. This simulates a DB that was created before the

packages/core/src/__tests__/mission-store.test.ts

@@ -2821,7 +2821,7 @@ describe("MissionStore", () => {
 
   describe("Loop State & Validator Run Schema (v31)", () => {
     it("schema version is 40 after migration", () => {
-      expect(db.getSchemaVersion()).toBe(87);
+      expect(db.getSchemaVersion()).toBe(88);
     });
 
     it("mission_features table has loop state columns", () => {

packages/core/src/__tests__/run-audit.test.ts

@@ -584,7 +584,7 @@ describe("Run Audit", () => {
     });
 
     it("schema version is bumped to 40", () => {
-      expect(db.getSchemaVersion()).toBe(87);
+      expect(db.getSchemaVersion()).toBe(88);
     });
   });
 });

packages/core/src/__tests__/secrets-schema.test.ts

@@ -42,7 +42,7 @@ describe("secrets schema migrations", () => {
       const version = db
         .prepare("SELECT value FROM __meta WHERE key = 'schemaVersion'")
         .get() as { value: string };
-      expect(version.value).toBe("87");
+      expect(version.value).toBe("88");
     } finally {
       db.close();
       rmSync(dir, { recursive: true, force: true });
@@ -105,7 +105,7 @@ describe("secrets schema migrations", () => {
       const version = db
         .prepare("SELECT value FROM __meta WHERE key = 'schemaVersion'")
         .get() as { value: string };
-      expect(version.value).toBe("87");
+      expect(version.value).toBe("88");
     } finally {
       db.close();
       rmSync(dir, { recursive: true, force: true });
@@ -155,7 +155,7 @@ describe("secrets schema migrations", () => {
         .prepare("SELECT value FROM __meta WHERE key = 'schemaVersion'")
         .get() as { value: string };
 
-      expect(projectVersion.value).toBe("87");
+      expect(projectVersion.value).toBe("88");
       expect(centralVersion.value).toBe("13");
     } finally {
       projectDb.close();

packages/core/src/__tests__/store-activity.test.ts

@@ -488,13 +488,19 @@ describe("TaskStore", () => {
       expect(task.pausedReason).toBeUndefined();
     };
 
+    async function moveTaskToDone(id: string): Promise<void> {
+      await store.moveTask(id, "todo");
+      await store.moveTask(id, "in-progress");
+      await store.moveTask(id, "in-review");
+      await store.moveTask(id, "done");
+    }
+
     it("clears pause fields on moveTask(in-review → done)", async () => {
       const task = await createTestTask();
       await store.moveTask(task.id, "todo");
       await store.moveTask(task.id, "in-progress");
       await store.moveTask(task.id, "in-review");
       await store.updateTask(task.id, {
-        paused: true,
         pausedByAgentId: "agent-x",
         pausedReason: "manual-hold",
       });
@@ -517,7 +523,7 @@ describe("TaskStore", () => {
 
     it("clears pause fields when mergeTask handles an already-done task", async () => {
       const task = await createTestTask();
-      await store.moveTask(task.id, "done");
+      await moveTaskToDone(task.id);
       await store.updateTask(task.id, { paused: true, pausedByAgentId: "agent-x" });
 
       await store.mergeTask(task.id);
@@ -527,9 +533,9 @@ describe("TaskStore", () => {
 
     it("clears pause fields on unarchiveTask transition to done", async () => {
       const task = await createTestTask();
-      await store.moveTask(task.id, "done");
-      await store.archiveTask(task.id);
+      await moveTaskToDone(task.id);
       await store.updateTask(task.id, { paused: true, pausedByAgentId: "agent-x", pausedReason: "manual-hold" });
+      await store.archiveTask(task.id);
 
       await store.unarchiveTask(task.id);
       const restored = await store.getTask(task.id);
@@ -539,8 +545,7 @@ describe("TaskStore", () => {
 
     it("remains idempotent across repeated done transitions", async () => {
       const task = await createTestTask();
-      await store.moveTask(task.id, "todo");
-      await store.moveTask(task.id, "done");
+      await moveTaskToDone(task.id);
       await store.moveTask(task.id, "archived");
       await store.updateTask(task.id, { paused: true, pausedByAgentId: "agent-x" });
 

packages/core/src/__tests__/task-documents.test.ts

@@ -51,7 +51,7 @@ describe("TaskStore task documents", () => {
 
     expect(tableNames.has("task_documents")).toBe(true);
     expect(tableNames.has("task_document_revisions")).toBe(true);
-    expect(db.getSchemaVersion()).toBe(87);
+    expect(db.getSchemaVersion()).toBe(88);
 
     const index = db
       .prepare(

packages/core/src/db.ts

@@ -3436,6 +3436,13 @@ export class Database {
     if (version < 88) {
       this.applyMigration(88, () => {
         try {
+          const taskColumns = this.getTableColumns("tasks");
+          const requiredColumns = ["paused", "userPaused", "pausedByAgentId", "pausedReason"];
+          if (!requiredColumns.every((column) => taskColumns.has(column))) {
+            console.log("[done-paused-backfill] db.ts migration skipped (missing paused columns on legacy schema)");
+            return;
+          }
+
           const result = this.db
             .prepare(`UPDATE tasks
                 SET paused = 0,

packages/core/src/store.ts

@@ -6519,15 +6519,19 @@ export class TaskStore extends EventEmitter<TaskStoreEvents> {
       const repairedTaskIds: string[] = [];
       for (const [taskId, cachedTask] of this.taskCache.entries()) {
         if (cachedTask.column !== "done") continue;
-        if (!this.clearDoneTransientFields(cachedTask)) continue;
 
-        await this.atomicWriteTaskJson(this.taskDir(taskId), cachedTask);
-        this.taskCache.set(taskId, { ...cachedTask });
+        const taskDir = this.taskDir(taskId);
+        const raw = await readFile(join(taskDir, "task.json"), "utf-8");
+        const diskTask = JSON.parse(raw) as Task;
+        if (!this.clearDoneTransientFields(diskTask)) continue;
+
+        await this.atomicWriteTaskJson(taskDir, diskTask);
+        this.taskCache.set(taskId, { ...diskTask });
         repairedTaskIds.push(taskId);
       }
       this.donePauseBackfillDone = true;
 
-      storeLog.info("done-task pause metadata backfill completed", {
+      storeLog.log("done-task pause metadata backfill completed", {
         phase: "watch:done-pause-backfill",
         repairedCount: repairedTaskIds.length,
         repairedTaskIds: repairedTaskIds.slice(0, 20),