refactor(daemon): upgrade Drizzle v1.0-beta + migrate better-sqlite3 → node:sqlite

- Upgrade drizzle-orm from 0.43.1 to 1.0.0-beta.23
- Replace better-sqlite3 with node:sqlite (DatabaseSync) in:
  - sense-runtime.ts (Drizzle driver)
  - log-store.ts (raw SQL)
  - all test files
- Replace sqlite.pragma() with sqlite.exec('PRAGMA ...')
- Replace sqlite.transaction() with manual BEGIN/COMMIT/ROLLBACK
- Update CLI init command to verify node:sqlite instead of better-sqlite3
- Remove better-sqlite3 and @types/better-sqlite3 from dependencies
- Zero native addons remaining in the monorepo 🎉

Closes #67

小橘 <xiaoju@shazhou.work>

packages/cli/src/commands/init.ts

@@ -1,4 +1,4 @@
-import { spawn, execFile } from "node:child_process";
+import { execFile, spawn } from "node:child_process";
 import { existsSync, mkdirSync, writeFileSync } from "node:fs";
 import { dirname, join } from "node:path";
 import { promisify } from "node:util";
@@ -35,7 +35,7 @@ const PACKAGE_JSON = `{
     "drizzle-kit": "latest"
   },
   "pnpm": {
-    "onlyBuiltDependencies": ["better-sqlite3", "esbuild"]
+    "onlyBuiltDependencies": ["esbuild"]
   }
 }
 `;
@@ -218,14 +218,18 @@ const initWorkspaceCommand = defineCommand({
   },
 });
 
-async function tryRequireSqlite(nerveRoot: string): Promise<boolean> {
+/** Verify built-in `node:sqlite` (Node.js ≥22.5) loads in a child process. */
+async function verifyNodeSqlite(): Promise<boolean> {
   try {
-    const modulePath = join(nerveRoot, "node_modules", "better-sqlite3");
-    // Use a child process to test if the native module loads
-    await execFileAsync("node", ["-e", `require(${JSON.stringify(modulePath)})`], {
-      cwd: nerveRoot,
-      timeout: 10_000,
-    });
+    await execFileAsync(
+      "node",
+      [
+        "--input-type=module",
+        "-e",
+        "import { DatabaseSync } from 'node:sqlite'; new DatabaseSync(':memory:').exec('SELECT 1');",
+      ],
+      { timeout: 10_000 },
+    );
     return true;
   } catch {
     return false;
@@ -264,27 +268,11 @@ async function runInitWorkspace(force: boolean): Promise<void> {
     );
   }
 
-  // Verify better-sqlite3 native module — rebuild up to 2 times if broken
-  const sqlitePath = join(nerveRoot, "node_modules", "better-sqlite3");
-  if (existsSync(sqlitePath)) {
-    for (let attempt = 1; attempt <= 2; attempt++) {
-      if (await tryRequireSqlite(nerveRoot)) break;
-      process.stdout.write(
-        `${attempt === 1 ? "Building" : "Retrying build of"} native module better-sqlite3 (attempt ${attempt}/2)…\n`,
-      );
-      try {
-        await runCommand(cmd, ["rebuild", "better-sqlite3"], nerveRoot);
-      } catch {
-        // will be caught by the verify below
-      }
-    }
-    if (!(await tryRequireSqlite(nerveRoot))) {
-      process.stdout.write(
-        `⚠️ better-sqlite3 native module is not working. The daemon will fail to start.\n` +
-          `   Fix: cd ${nerveRoot} && ${cmd} rebuild better-sqlite3\n` +
-          `   Or:  npm install --build-from-source better-sqlite3\n`,
-      );
-    }
+  if (!(await verifyNodeSqlite())) {
+    process.stdout.write(
+      "⚠️ Built-in SQLite (node:sqlite) is not available in this Node.js build. " +
+        "The daemon requires Node.js 22.5 or newer with SQLite enabled.\n",
+    );
   }
 
   if (!existsSync(join(nerveRoot, ".git"))) {

packages/daemon/package.json

@@ -17,12 +17,11 @@
   },
   "dependencies": {
     "@uncaged/nerve-core": "workspace:*",
-    "better-sqlite3": "^11.10.0",
-    "drizzle-orm": "^0.43.1",
+    "drizzle-orm": "1.0.0-beta.23-c10d10c",
     "yaml": "^2.8.3"
   },
   "devDependencies": {
-    "@types/better-sqlite3": "^7.6.13",
+    "@types/node": "^22.0.0",
     "vitest": "^4.1.5"
   }
 }

packages/daemon/src/__tests__/kernel-trigger-sense.test.ts

@@ -2,7 +2,7 @@
  * Unit tests for kernel.triggerSense() — IPC issue #36.
  *
  * These tests use a mock child_process and a mock LogStore so they do NOT
- * require better-sqlite3 to be present in the test environment.
+ * require a real LogStore (node:sqlite) in integration tests.
  */
 
 import { EventEmitter } from "node:events";
@@ -58,7 +58,7 @@ vi.mock("node:child_process", () => ({
 const { createKernel } = await import("../kernel.js");
 
 // ---------------------------------------------------------------------------
-// Mock LogStore factory (avoids better-sqlite3 dependency)
+// Mock LogStore factory (avoids SQLite I/O in this unit test)
 // ---------------------------------------------------------------------------
 
 function makeMockLogStore() {

packages/daemon/src/__tests__/sense-runtime.test.ts

@@ -2,8 +2,8 @@ import { mkdirSync, mkdtempSync, writeFileSync } from "node:fs";
 import { tmpdir } from "node:os";
 import { join } from "node:path";
 
-import Database from "better-sqlite3";
-import { drizzle } from "drizzle-orm/better-sqlite3";
+import { DatabaseSync } from "node:sqlite";
+import { drizzle } from "drizzle-orm/node-sqlite";
 import { integer, real, sqliteTable } from "drizzle-orm/sqlite-core";
 import { describe, expect, it } from "vitest";
 
@@ -49,7 +49,7 @@ const samples = sqliteTable("samples", {
 
 describe("runMigrations", () => {
   it("creates table via SQL migration file", () => {
-    const sqlite = new Database(":memory:");
+    const sqlite = new DatabaseSync(":memory:");
     const migrationsDir = makeTempMigrationsDir(INIT_SQL);
     const result = runMigrations(sqlite, migrationsDir);
 
@@ -64,7 +64,7 @@ describe("runMigrations", () => {
   });
 
   it("runs multiple migrations in lexicographic order", () => {
-    const sqlite = new Database(":memory:");
+    const sqlite = new DatabaseSync(":memory:");
     const dir = mkdtempSync(join(tmpdir(), "nerve-multi-"));
 
     writeFileSync(join(dir, "0001_init.sql"), INIT_SQL);
@@ -81,7 +81,7 @@ describe("runMigrations", () => {
   });
 
   it("returns ok when migrations directory is empty", () => {
-    const sqlite = new Database(":memory:");
+    const sqlite = new DatabaseSync(":memory:");
     const dir = makeTempMigrationsDirEmpty();
     const result = runMigrations(sqlite, dir);
     expect(result.ok).toBe(true);
@@ -89,14 +89,14 @@ describe("runMigrations", () => {
   });
 
   it("returns err when migrations directory does not exist", () => {
-    const sqlite = new Database(":memory:");
+    const sqlite = new DatabaseSync(":memory:");
     const result = runMigrations(sqlite, "/nonexistent/path/migrations");
     expect(result.ok).toBe(false);
     sqlite.close();
   });
 
   it("returns err when a migration SQL is invalid", () => {
-    const sqlite = new Database(":memory:");
+    const sqlite = new DatabaseSync(":memory:");
     const dir = mkdtempSync(join(tmpdir(), "nerve-bad-sql-"));
     writeFileSync(join(dir, "0001_bad.sql"), "NOT VALID SQL !!!;");
     const result = runMigrations(sqlite, dir);
@@ -141,7 +141,7 @@ describe("openPeerDb", () => {
   it("opens an existing db in read-only mode", () => {
     // Create a writable db first
     const dbPath = makeTempDbPath();
-    const sqlite = new Database(dbPath);
+    const sqlite = new DatabaseSync(dbPath);
     sqlite.exec(INIT_SQL);
     sqlite.prepare("INSERT INTO samples (ts, value) VALUES (1, 42.0)").run();
     sqlite.close();
@@ -170,11 +170,11 @@ describe("openPeerDb", () => {
 describe("executeCompute", () => {
   function makeRuntime(computeFn: ComputeFn): {
     runtime: SenseRuntime;
-    sqlite: Database.Database;
+    sqlite: DatabaseSync;
   } {
-    const sqlite = new Database(":memory:");
+    const sqlite = new DatabaseSync(":memory:");
     sqlite.exec(INIT_SQL);
-    const db = drizzle(sqlite) as DrizzleDB;
+    const db = drizzle({ client: sqlite }) as DrizzleDB;
     return {
       runtime: { name: "test-sense", db, compute: computeFn },
       sqlite,
@@ -226,10 +226,10 @@ describe("executeCompute", () => {
 
   it("compute can read from peers", async () => {
     // Set up a peer db with data
-    const peerSqlite = new Database(":memory:");
+    const peerSqlite = new DatabaseSync(":memory:");
     peerSqlite.exec(INIT_SQL);
     peerSqlite.prepare("INSERT INTO samples (ts, value) VALUES (100, 3.14)").run();
-    const peerDb = drizzle(peerSqlite) as DrizzleDB;
+    const peerDb = drizzle({ client: peerSqlite }) as DrizzleDB;
 
     const peers: PeerMap = { "other-sense": peerDb };
 
@@ -248,9 +248,9 @@ describe("executeCompute", () => {
   });
 
   it("write to own db does not affect peer db (isolation)", async () => {
-    const peerSqlite = new Database(":memory:");
+    const peerSqlite = new DatabaseSync(":memory:");
     peerSqlite.exec(INIT_SQL);
-    const peerDb = drizzle(peerSqlite) as DrizzleDB;
+    const peerDb = drizzle({ client: peerSqlite }) as DrizzleDB;
     const peers: PeerMap = { "peer-sense": peerDb };
 
     const { runtime, sqlite } = makeRuntime(async (db) => {
@@ -403,7 +403,7 @@ describe("parseParentMessage", () => {
 
 describe("runMigrations journal", () => {
   it("does not re-run an already-applied migration", () => {
-    const sqlite = new Database(":memory:");
+    const sqlite = new DatabaseSync(":memory:");
     const dir = mkdtempSync(join(tmpdir(), "nerve-journal-"));
     writeFileSync(join(dir, "0001_init.sql"), INIT_SQL);
 
@@ -430,7 +430,7 @@ describe("runMigrations journal", () => {
   });
 
   it("tracks migrations in _migrations table", () => {
-    const sqlite = new Database(":memory:");
+    const sqlite = new DatabaseSync(":memory:");
     const dir = mkdtempSync(join(tmpdir(), "nerve-journal2-"));
     writeFileSync(join(dir, "0001_init.sql"), INIT_SQL);
 

packages/daemon/src/log-store.ts

@@ -9,8 +9,7 @@
 
 import { mkdirSync, writeFileSync } from "node:fs";
 import { dirname, join } from "node:path";
-import Database from "better-sqlite3";
-import type BetterSqlite3 from "better-sqlite3";
+import { DatabaseSync, type StatementSync } from "node:sqlite";
 
 import {
   DEFAULT_LOG_RETENTION_MS,
@@ -184,7 +183,23 @@ function buildJsonlBody(rows: SqlLogRow[]): string {
   return `${lines.join("\n")}\n`;
 }
 
-function runOptionalVacuum(sqlite: BetterSqlite3.Database, vacuum?: boolean): boolean {
+function runInTransaction<T>(db: DatabaseSync, fn: () => T): T {
+  db.exec("BEGIN IMMEDIATE");
+  try {
+    const out = fn();
+    db.exec("COMMIT");
+    return out;
+  } catch (e) {
+    try {
+      db.exec("ROLLBACK");
+    } catch {
+      // ignore rollback errors
+    }
+    throw e;
+  }
+}
+
+function runOptionalVacuum(sqlite: DatabaseSync, vacuum?: boolean): boolean {
   if (vacuum !== true) return false;
   sqlite.exec("VACUUM");
   return true;
@@ -199,7 +214,7 @@ function resolveArchiveStartDay(watermark: string | null, minDay: string): strin
 function runArchiveDayLoop(
   dbPath: string,
   options: ArchiveLogsOptions,
-  selectLogsForDayStmt: BetterSqlite3.Statement,
+  selectLogsForDayStmt: StatementSync,
   archiveDayTx: (day: string, start: number, endExclusive: number) => void,
   startDay: string,
   lastDay: string,
@@ -235,8 +250,8 @@ function runArchiveDayLoop(
 export function createLogStore(dbPath: string): LogStore {
   mkdirSync(dirname(dbPath), { recursive: true });
 
-  const sqlite: BetterSqlite3.Database = new Database(dbPath);
-  sqlite.pragma("journal_mode = WAL");
+  const sqlite = new DatabaseSync(dbPath);
+  sqlite.exec("PRAGMA journal_mode=WAL");
   sqlite.exec(SCHEMA_SQL);
 
   const insertStmt = sqlite.prepare(
@@ -288,8 +303,8 @@ export function createLogStore(dbPath: string): LogStore {
     "DELETE FROM logs WHERE ts >= @start AND ts < @endExclusive",
   );
 
-  const upsertWorkflowRunTx = sqlite.transaction(
-    (entry: Omit<LogEntry, "id">, run: WorkflowRun) => {
+  function upsertWorkflowRunTx(entry: Omit<LogEntry, "id">, run: WorkflowRun): LogEntry {
+    return runInTransaction(sqlite, () => {
       const info = insertStmt.run({
         source: entry.source,
         type: entry.type,
@@ -304,8 +319,8 @@ export function createLogStore(dbPath: string): LogStore {
         ts: run.ts,
       });
       return { ...entry, id: Number(info.lastInsertRowid) };
-    },
-  );
+    });
+  }
 
   function append(entry: Omit<LogEntry, "id">): LogEntry {
     const info = insertStmt.run({
@@ -376,11 +391,11 @@ export function createLogStore(dbPath: string): LogStore {
   }
 
   function upsertWorkflowRun(entry: Omit<LogEntry, "id">, run: WorkflowRun): LogEntry {
-    return upsertWorkflowRunTx(entry, run) as LogEntry;
+    return upsertWorkflowRunTx(entry, run);
   }
 
   function appendWithWorkflowUpdate(entry: Omit<LogEntry, "id">, run: WorkflowRun): LogEntry {
-    return upsertWorkflowRunTx(entry, run) as LogEntry;
+    return upsertWorkflowRunTx(entry, run);
   }
 
   function getWorkflowRun(runId: string): WorkflowRun | null {
@@ -460,10 +475,12 @@ export function createLogStore(dbPath: string): LogStore {
     return result;
   }
 
-  const archiveDayTx = sqlite.transaction((day: string, start: number, endExclusive: number) => {
-    deleteLogsForDayStmt.run({ start, endExclusive });
-    setMetaStmt.run({ key: LOG_ARCHIVE_META_KEY, value: day });
-  });
+  function archiveDayTx(day: string, start: number, endExclusive: number): void {
+    runInTransaction(sqlite, () => {
+      deleteLogsForDayStmt.run({ start, endExclusive });
+      setMetaStmt.run({ key: LOG_ARCHIVE_META_KEY, value: day });
+    });
+  }
 
   function readWatermark(): string | null {
     const raw = getMeta(LOG_ARCHIVE_META_KEY);

packages/daemon/src/sense-runtime.ts

@@ -1,9 +1,9 @@
 import { mkdirSync, readFileSync, readdirSync } from "node:fs";
 import { dirname, join } from "node:path";
+import { DatabaseSync } from "node:sqlite";
 
-import Database from "better-sqlite3";
-import { drizzle } from "drizzle-orm/better-sqlite3";
-import type { BetterSQLite3Database } from "drizzle-orm/better-sqlite3";
+import { drizzle } from "drizzle-orm/node-sqlite";
+import type { NodeSQLiteDatabase } from "drizzle-orm/node-sqlite";
 
 import type { Result } from "@uncaged/nerve-core";
 import { err, ok } from "@uncaged/nerve-core";
@@ -11,7 +11,7 @@ import { err, ok } from "@uncaged/nerve-core";
 import type { BlobStore } from "./blob-store.js";
 
 /** A Drizzle DB instance (schema-generic) */
-export type DrizzleDB = BetterSQLite3Database<Record<string, never>>;
+export type DrizzleDB = NodeSQLiteDatabase<Record<string, never>>;
 
 /** Read-only map of peer sense name → their Drizzle DB */
 export type PeerMap = Readonly<Record<string, DrizzleDB>>;
@@ -42,7 +42,7 @@ export type SenseRuntime = {
   compute: ComputeFn;
 };
 
-function ensureMigrationsTable(sqlite: Database.Database): Result<void> {
+function ensureMigrationsTable(sqlite: DatabaseSync): Result<void> {
   try {
     sqlite.exec(
       `CREATE TABLE IF NOT EXISTS _migrations (
@@ -69,11 +69,7 @@ function listMigrationFiles(migrationsDir: string): Result<string[]> {
   }
 }
 
-function applyMigrationFile(
-  sqlite: Database.Database,
-  file: string,
-  filePath: string,
-): Result<void> {
+function applyMigrationFile(sqlite: DatabaseSync, file: string, filePath: string): Result<void> {
   let sql: string;
   try {
     sql = readFileSync(filePath, "utf8");
@@ -83,13 +79,18 @@ function applyMigrationFile(
   }
 
   const insertJournal = sqlite.prepare("INSERT INTO _migrations (name, applied_at) VALUES (?, ?)");
+  sqlite.exec("BEGIN IMMEDIATE");
   try {
-    sqlite.transaction(() => {
-      sqlite.exec(sql);
-      insertJournal.run(file, Date.now());
-    })();
+    sqlite.exec(sql);
+    insertJournal.run(file, Date.now());
+    sqlite.exec("COMMIT");
     return ok(undefined);
   } catch (e) {
+    try {
+      sqlite.exec("ROLLBACK");
+    } catch {
+      // ignore secondary errors during rollback
+    }
     const msg = e instanceof Error ? e.message : String(e);
     return err(new Error(`Migration "${file}" failed: ${msg}`));
   }
@@ -97,10 +98,10 @@ function applyMigrationFile(
 
 /**
  * Run all *.sql migration files in the given directory against a
- * better-sqlite3 Database, in lexicographic order.
+ * `node:sqlite` DatabaseSync, in lexicographic order.
  * Tracks applied migrations in _migrations table to avoid re-running.
  */
-export function runMigrations(sqlite: Database.Database, migrationsDir: string): Result<void> {
+export function runMigrations(sqlite: DatabaseSync, migrationsDir: string): Result<void> {
   const tableResult = ensureMigrationsTable(sqlite);
   if (!tableResult.ok) return tableResult;
 
@@ -129,14 +130,13 @@ export function runMigrations(sqlite: Database.Database, migrationsDir: string):
 export function openSenseDb(
   dbPath: string,
   migrationsDir: string,
-): Result<{ sqlite: Database.Database; db: DrizzleDB }> {
-  let sqlite: Database.Database;
+): Result<{ sqlite: DatabaseSync; db: DrizzleDB }> {
+  let sqlite: DatabaseSync;
 
   try {
     mkdirSync(dirname(dbPath), { recursive: true });
-    sqlite = new Database(dbPath);
-    // WAL mode for better concurrent read performance
-    sqlite.pragma("journal_mode = WAL");
+    sqlite = new DatabaseSync(dbPath);
+    sqlite.exec("PRAGMA journal_mode=WAL");
   } catch (e) {
     const msg = e instanceof Error ? e.message : String(e);
     return err(new Error(`Failed to open database "${dbPath}": ${msg}`));
@@ -145,7 +145,7 @@ export function openSenseDb(
   const migResult = runMigrations(sqlite, migrationsDir);
   if (!migResult.ok) return migResult;
 
-  const db = drizzle(sqlite) as DrizzleDB;
+  const db = drizzle({ client: sqlite }) as DrizzleDB;
   return ok({ sqlite, db });
 }
 
@@ -153,16 +153,16 @@ export function openSenseDb(
  * Open a peer sense DB in read-only mode (no migrations).
  */
 export function openPeerDb(dbPath: string): Result<DrizzleDB> {
-  let sqlite: Database.Database;
+  let sqlite: DatabaseSync;
 
   try {
-    sqlite = new Database(dbPath, { readonly: true });
+    sqlite = new DatabaseSync(dbPath, { readOnly: true });
   } catch (e) {
     const msg = e instanceof Error ? e.message : String(e);
     return err(new Error(`Failed to open peer database "${dbPath}" (readonly): ${msg}`));
   }
 
-  return ok(drizzle(sqlite) as DrizzleDB);
+  return ok(drizzle({ client: sqlite }) as DrizzleDB);
 }
 
 /**

pnpm-workspace.yaml

@@ -3,5 +3,4 @@ packages:
 
 onlyBuiltDependencies:
   - "@biomejs/biome"
-  - better-sqlite3
   - esbuild