Refactor application module architecture for clarity and explicitness (#18432)

## Summary

- **Module reorganization**: Moved `ApplicationUpgradeService` and cron
jobs to `application-upgrade/`, `ApplicationSyncService` to
`application-manifest/`, and
`runWorkspaceMigration`/`uninstallApplication` mutations to the manifest
resolver — each module now has a single clear responsibility.
- **Explicit install flow**: Removed implicit `ApplicationEntity`
creation from `ApplicationSyncService`. The install service and dev
resolver now explicitly create the `ApplicationEntity` before syncing.
npm packages are resolved at registration time to extract manifest
metadata (universalIdentifier, name, description, etc.), eliminating the
`reconcileUniversalIdentifier` hack.
- **Better error handling**: Frontend hooks now surface actual server
error messages in snackbars instead of swallowing them. Replaced the
ugly `ConfirmationModal` for transfer ownership with a proper form
modal. Fixed `SettingsAdminTableCard` row height overflow and corrected
the `yarn-engine` asset path.

## Test plan
- [ ] Register an npm package — verify manifest metadata (name,
description, universalIdentifier) is extracted correctly
- [ ] Install a registered npm app on a workspace — verify
ApplicationEntity is created and sync succeeds
- [ ] Test `app:dev` CLI flow — verify local app registration and sync
work
- [ ] Upload a tarball — verify registration and install flow
- [ ] Transfer ownership — verify the new modal UX works
- [ ] Verify error messages appear correctly in snackbars when
operations fail


Made with [Cursor](https://cursor.com)

packages/twenty-server/src/engine/metadata-modules/permissions/__tests__/permissions.service.spec.ts

@@ -4,7 +4,7 @@ import { getRepositoryToken } from '@nestjs/typeorm';
 import { PermissionFlagType } from 'twenty-shared/constants';
 
 import { ApiKeyRoleService } from 'src/engine/core-modules/api-key/services/api-key-role.service';
-import { ApplicationService } from 'src/engine/core-modules/application/application.service';
+import { ApplicationEntity } from 'src/engine/core-modules/application/application.entity';
 import { PermissionsService } from 'src/engine/metadata-modules/permissions/permissions.service';
 import { RoleEntity } from 'src/engine/metadata-modules/role/role.entity';
 import { UserRoleService } from 'src/engine/metadata-modules/user-role/user-role.service';
@@ -34,7 +34,7 @@ describe('PermissionsService', () => {
           useValue: {},
         },
         {
-          provide: ApplicationService,
+          provide: getRepositoryToken(ApplicationEntity),
           useValue: {},
         },
       ],

packages/twenty-server/src/engine/metadata-modules/permissions/permissions.module.ts

@@ -4,7 +4,6 @@ import { TypeOrmModule } from '@nestjs/typeorm';
 import { ApiKeyEntity } from 'src/engine/core-modules/api-key/api-key.entity';
 import { ApiKeyRoleService } from 'src/engine/core-modules/api-key/services/api-key-role.service';
 import { ApplicationEntity } from 'src/engine/core-modules/application/application.entity';
-import { ApplicationModule } from 'src/engine/core-modules/application/application.module';
 import { FeatureFlagModule } from 'src/engine/core-modules/feature-flag/feature-flag.module';
 import { UserWorkspaceEntity } from 'src/engine/core-modules/user-workspace/user-workspace.entity';
 import { PermissionsService } from 'src/engine/metadata-modules/permissions/permissions.service';
@@ -27,7 +26,6 @@ import { WorkspaceCacheModule } from 'src/engine/workspace-cache/workspace-cache
     UserRoleModule,
     WorkspaceCacheModule,
     RoleTargetModule,
-    ApplicationModule,
   ],
   providers: [ApiKeyRoleService, PermissionsService],
   exports: [PermissionsService, ApiKeyRoleService],

packages/twenty-server/src/engine/metadata-modules/permissions/permissions.service.ts

@@ -7,7 +7,11 @@ import { isDefined } from 'twenty-shared/utils';
 import { In, Repository } from 'typeorm';
 
 import { ApiKeyRoleService } from 'src/engine/core-modules/api-key/services/api-key-role.service';
-import { ApplicationService } from 'src/engine/core-modules/application/application.service';
+import { ApplicationEntity } from 'src/engine/core-modules/application/application.entity';
+import {
+  ApplicationException,
+  ApplicationExceptionCode,
+} from 'src/engine/core-modules/application/application.exception';
 import { TOOL_PERMISSION_FLAGS } from 'src/engine/metadata-modules/permissions/constants/tool-permission-flags';
 import {
   PermissionsException,
@@ -28,7 +32,8 @@ export class PermissionsService {
     private readonly apiKeyRoleService: ApiKeyRoleService,
     @InjectRepository(RoleEntity)
     private readonly roleRepository: Repository<RoleEntity>,
-    private readonly applicationService: ApplicationService,
+    @InjectRepository(ApplicationEntity)
+    private readonly applicationRepository: Repository<ApplicationEntity>,
   ) {}
 
   private isToolPermission(feature: string) {
@@ -183,11 +188,18 @@ export class PermissionsService {
     }
 
     if (applicationId) {
-      const applicationRoleId =
-        await this.applicationService.findApplicationRoleId(
-          applicationId,
-          workspaceId,
+      const application = await this.applicationRepository.findOne({
+        where: { id: applicationId, workspaceId },
+      });
+
+      if (!isDefined(application) || !isDefined(application.defaultRoleId)) {
+        throw new ApplicationException(
+          `Could not find application ${applicationId}`,
+          ApplicationExceptionCode.APPLICATION_NOT_FOUND,
         );
+      }
+
+      const applicationRoleId = application.defaultRoleId;
 
       const role = await this.roleRepository.findOne({
         where: { id: applicationRoleId, workspaceId },