build: allow node package depends on workspace packages (#11963)

<!-- This is an auto-generated comment: release notes by coderabbit.ai -->
## Summary by CodeRabbit

- **New Features**
  - Added a unified CLI entry point for server operations and introduced a new CLI executable alias.
  - Centralized and simplified server startup, allowing selection between CLI and server modes.
  - Added static migration module aggregation for easier migration management.

- **Bug Fixes**
  - Improved platform-specific native module loading for better compatibility and reliability.

- **Refactor**
  - Streamlined server build, startup, and artifact management processes.
  - Reorganized and simplified workflow and configuration files for backend services.
  - Transitioned export styles and import mechanisms for native modules to enhance maintainability.

- **Chores**
  - Removed unused dependencies and configuration files.
  - Updated test cases to reflect refined server flavor logic.
  - Adjusted package and build configurations for consistency and clarity.

- **Revert**
  - Removed legacy scripts and loaders no longer needed after refactor.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

tools/utils/src/workspace.gen.ts

@@ -963,10 +963,10 @@ export const PackageList = [
     location: 'packages/backend/server',
     name: '@affine/server',
     workspaceDependencies: [
+      'packages/backend/native',
       'tools/cli',
       'tools/utils',
       'packages/common/graphql',
-      'packages/backend/native',
     ],
   },
   {