fix(core): finish deferred agentLogEntries drop when migrations 103+ outrun it

Migration 102 defers the destructive agentLogEntries drop until TaskStore
copies legacy rows to JSONL and writes the __meta guard, then relies on a
second init() pass gated on schemaVersion < SCHEMA_VERSION. Migrations
103-105 bump the version to 105 on the first pass, so the second pass never
fired and the legacy table survived forever. Make the drop version-independent
in migrate() and trigger the re-init whenever the legacy table remains.

Also pin secrets-schema.test.ts to String(SCHEMA_VERSION) instead of the
hardcoded "102" string the schema bump invalidated.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

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

@@ -2,7 +2,7 @@ import { describe, it, expect } from "vitest";
 import { mkdtempSync, rmSync } from "node:fs";
 import { tmpdir } from "node:os";
 import { join } from "node:path";
-import { Database } from "../db.js";
+import { Database, SCHEMA_VERSION } from "../db.js";
 import { createCentralDatabase } from "../central-db.js";
 
 function createTempDir(prefix: string): string {
@@ -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("102");
+      expect(version.value).toBe(String(SCHEMA_VERSION));
     } 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("102");
+      expect(version.value).toBe(String(SCHEMA_VERSION));
     } 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("102");
+      expect(projectVersion.value).toBe(String(SCHEMA_VERSION));
       expect(centralVersion.value).toBe("13");
     } finally {
       projectDb.close();

packages/core/src/db.ts

@@ -2028,6 +2028,28 @@ export class Database {
       this.addColumnIfMissing("tasks", "scopeAutoWiden", "TEXT DEFAULT '[]'");
     }
 
+    // Deferred agentLogEntries drop (companion to migration 102): when the
+    // legacy table still had rows on the first init pass, the destructive drop
+    // was deferred until TaskStore copies the rows to JSONL and writes the
+    // __meta guard, then re-runs init(). Migrations 103+ bump the schema
+    // version past 102 on that first pass, so the re-run can no longer reach
+    // the version-gated 102 block — finish the drop here, version-independent
+    // (and before the early return below, which fires once the version is
+    // current).
+    if (this.hasTable("agentLogEntries")) {
+      const agentLogMigrationComplete = this.getMetaValue("agentLogEntriesToFileMigrationVersion") === "1";
+      const legacyAgentLogTableIsEmpty =
+        (this.db.prepare("SELECT COUNT(*) as count FROM agentLogEntries").get() as { count: number }).count === 0;
+      const hasLegacyAgentLogCitations = this.hasTable("goal_citations")
+        ? (this.db.prepare(
+            "SELECT 1 FROM goal_citations WHERE surface = 'agent_log' AND sourceRef GLOB 'agentLog:[0-9]*' LIMIT 1",
+          ).get() ?? undefined) !== undefined
+        : false;
+      if (agentLogMigrationComplete || (legacyAgentLogTableIsEmpty && !hasLegacyAgentLogCitations)) {
+        this.db.exec(`DROP TABLE IF EXISTS agentLogEntries`);
+      }
+    }
+
     if (version >= SCHEMA_VERSION) return;
 
     if (version < 2) {

packages/core/src/store.ts

@@ -1443,7 +1443,17 @@ export class TaskStore extends EventEmitter<TaskStoreEvents> {
     await this.migrateActiveArchivedTasksToArchiveDb();
     await this.migrateAgentLogEntriesToFilesOnce();
     await this.cleanupNoOpTaskMovedActivityRowsOnce();
-    if (this.db.getSchemaVersion() < SCHEMA_VERSION) {
+    // Re-run init when migrations are pending, or when the deferred
+    // agentLogEntries drop still needs to fire: migration 102 skips the
+    // destructive drop until migrateAgentLogEntriesToFilesOnce() above writes
+    // the __meta guard, but migrations 103+ bump the schema version past 102
+    // on the first pass, so the version check alone no longer triggers the
+    // second pass that performs the drop.
+    const legacyAgentLogTableRemains =
+      this.db
+        .prepare("SELECT 1 FROM sqlite_master WHERE type = 'table' AND name = 'agentLogEntries' LIMIT 1")
+        .get() !== undefined;
+    if (this.db.getSchemaVersion() < SCHEMA_VERSION || legacyAgentLogTableRemains) {
       this.db.init();
     }
     await this.importLegacyAgentLogsOnce();