diff --git a/packages/backend/server/package.json b/packages/backend/server/package.json
index bdf4630d2e..94e17998f3 100644
--- a/packages/backend/server/package.json
+++ b/packages/backend/server/package.json
@@ -15,8 +15,8 @@
     "test:copilot": "ava \"src/__tests__/**/copilot-*.spec.ts\"",
     "test:coverage": "c8 ava --concurrency 1 --serial",
     "test:copilot:coverage": "c8 ava --timeout=5m \"src/__tests__/**/copilot-*.spec.ts\"",
-    "data-migration": "cross-env NODE_ENV=script r ./src/data/index.ts",
-    "predeploy": "yarn prisma migrate deploy && NODE_ENV=script node --import ./scripts/register.js ./dist/data/index.js run",
+    "data-migration": "cross-env NODE_ENV=development r ./src/data/index.ts",
+    "predeploy": "yarn prisma migrate deploy && node --import ./scripts/register.js ./dist/data/index.js run",
     "postinstall": "prisma generate"
   },
   "dependencies": {
diff --git a/packages/backend/server/src/__tests__/app/doc.e2e.ts b/packages/backend/server/src/__tests__/app/doc.e2e.ts
index b63626a087..c06860c224 100644
--- a/packages/backend/server/src/__tests__/app/doc.e2e.ts
+++ b/packages/backend/server/src/__tests__/app/doc.e2e.ts
@@ -19,6 +19,7 @@ test.before('start app', async t => {
     sync: false,
     renderer: false,
     doc: true,
+    script: false,
   } satisfies typeof AFFiNE.flavor;
   const app = await createTestingApp({
     imports: [buildAppModule()],
diff --git a/packages/backend/server/src/__tests__/app/graphql.e2e.ts b/packages/backend/server/src/__tests__/app/graphql.e2e.ts
index c22d208e15..2b8fa8b1a1 100644
--- a/packages/backend/server/src/__tests__/app/graphql.e2e.ts
+++ b/packages/backend/server/src/__tests__/app/graphql.e2e.ts
@@ -21,6 +21,7 @@ test.before('start app', async t => {
     sync: false,
     renderer: false,
     doc: false,
+    script: false,
   } satisfies typeof AFFiNE.flavor;
   const app = await createTestingApp({
     imports: [buildAppModule()],
diff --git a/packages/backend/server/src/__tests__/app/renderer.e2e.ts b/packages/backend/server/src/__tests__/app/renderer.e2e.ts
index d1edfb0fbe..900f011cda 100644
--- a/packages/backend/server/src/__tests__/app/renderer.e2e.ts
+++ b/packages/backend/server/src/__tests__/app/renderer.e2e.ts
@@ -19,6 +19,7 @@ test.before('start app', async t => {
     sync: false,
     renderer: true,
     doc: false,
+    script: false,
   } satisfies typeof AFFiNE.flavor;
   const app = await createTestingApp({
     imports: [buildAppModule()],
diff --git a/packages/backend/server/src/__tests__/app/sync.e2e.ts b/packages/backend/server/src/__tests__/app/sync.e2e.ts
index aa6a414b1e..b67ccd9f82 100644
--- a/packages/backend/server/src/__tests__/app/sync.e2e.ts
+++ b/packages/backend/server/src/__tests__/app/sync.e2e.ts
@@ -19,6 +19,7 @@ test.before('start app', async t => {
     sync: true,
     renderer: false,
     doc: false,
+    script: false,
   } satisfies typeof AFFiNE.flavor;
   const app = await createTestingApp({
     imports: [buildAppModule()],
diff --git a/packages/backend/server/src/base/config/def.ts b/packages/backend/server/src/base/config/def.ts
index 6e22163980..f25676c982 100644
--- a/packages/backend/server/src/base/config/def.ts
+++ b/packages/backend/server/src/base/config/def.ts
@@ -2,9 +2,16 @@ import type { LeafPaths } from '../utils/types';
 import { AppStartupConfig } from './types';
 
 export type EnvConfigType = 'string' | 'int' | 'float' | 'boolean';
-export type ServerFlavor = 'allinone' | 'graphql' | 'sync' | 'renderer' | 'doc';
+export type ServerFlavor =
+  | 'allinone'
+  | 'graphql'
+  | 'sync'
+  | 'renderer'
+  | 'doc'
+  | 'script';
+
 export type AFFINE_ENV = 'dev' | 'beta' | 'production';
-export type NODE_ENV = 'development' | 'test' | 'production' | 'script';
+export type NODE_ENV = 'development' | 'test' | 'production';
 
 export enum DeploymentType {
   Affine = 'affine',
@@ -29,7 +36,6 @@ export interface PreDefinedAFFiNEConfig {
     prod: boolean;
     dev: boolean;
     test: boolean;
-    script: boolean;
   };
   readonly deploy: boolean;
 }
diff --git a/packages/backend/server/src/base/config/default.ts b/packages/backend/server/src/base/config/default.ts
index 30cf58d003..51b1092bb6 100644
--- a/packages/backend/server/src/base/config/default.ts
+++ b/packages/backend/server/src/base/config/default.ts
@@ -13,12 +13,15 @@ import {
 import { readEnv } from './env';
 import { defaultStartupConfig } from './register';
 
+function expectFlavor(flavor: ServerFlavor, expected: ServerFlavor) {
+  return flavor === expected || flavor === 'allinone';
+}
+
 function getPredefinedAFFiNEConfig(): PreDefinedAFFiNEConfig {
   const NODE_ENV = readEnv<NODE_ENV>('NODE_ENV', 'production', [
     'development',
     'test',
     'production',
-    'script',
   ]);
   const AFFINE_ENV = readEnv<AFFINE_ENV>('AFFINE_ENV', 'production', [
     'dev',
@@ -31,6 +34,7 @@ function getPredefinedAFFiNEConfig(): PreDefinedAFFiNEConfig {
     'sync',
     'renderer',
     'doc',
+    'script',
   ]);
   const deploymentType = readEnv<DeploymentType>(
     'DEPLOYMENT_TYPE',
@@ -49,7 +53,6 @@ function getPredefinedAFFiNEConfig(): PreDefinedAFFiNEConfig {
     prod: NODE_ENV === 'production',
     dev: NODE_ENV === 'development',
     test: NODE_ENV === 'test',
-    script: NODE_ENV === 'script',
   };
 
   return {
@@ -64,10 +67,11 @@ function getPredefinedAFFiNEConfig(): PreDefinedAFFiNEConfig {
     flavor: {
       type: flavor,
       allinone: flavor === 'allinone',
-      graphql: flavor === 'graphql' || flavor === 'allinone',
-      sync: flavor === 'sync' || flavor === 'allinone',
-      renderer: flavor === 'renderer' || flavor === 'allinone',
-      doc: flavor === 'doc' || flavor === 'allinone',
+      graphql: expectFlavor(flavor, 'graphql'),
+      sync: expectFlavor(flavor, 'sync'),
+      renderer: expectFlavor(flavor, 'renderer'),
+      doc: expectFlavor(flavor, 'doc'),
+      script: expectFlavor(flavor, 'script'),
     },
     affine,
     node,
diff --git a/packages/backend/server/src/data/index.ts b/packages/backend/server/src/data/index.ts
index f9735c6e1a..3797a9badb 100644
--- a/packages/backend/server/src/data/index.ts
+++ b/packages/backend/server/src/data/index.ts
@@ -1,11 +1,10 @@
-import '../prelude';
-
 import { Logger } from '@nestjs/common';
 import { CommandFactory } from 'nest-commander';
 
 async function bootstrap() {
-  AFFiNE.metrics.enabled = false;
-  AFFiNE.doc.manager.enableUpdateAutoMerging = false;
+  process.env.SERVER_FLAVOR = 'script';
+
+  await import('../prelude');
   const { CliAppModule } = await import('./app');
   await CommandFactory.run(CliAppModule, new Logger()).catch(e => {
     console.error(e);