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/database/commands/database-command.module.ts

@@ -9,7 +9,7 @@ import { UpgradeVersionCommandModule } from 'src/database/commands/upgrade-versi
 import { TypeORMModule } from 'src/database/typeorm/typeorm.module';
 import { ApiKeyModule } from 'src/engine/core-modules/api-key/api-key.module';
 import { GenerateApiKeyCommand } from 'src/engine/core-modules/api-key/commands/generate-api-key.command';
-import { AppVersionCheckModule } from 'src/engine/core-modules/application/application-version-check/application-version-check.module';
+import { ApplicationUpgradeModule } from 'src/engine/core-modules/application/application-upgrade/application-upgrade.module';
 import { MarketplaceModule } from 'src/engine/core-modules/application/application-marketplace/marketplace.module';
 import { EventLogCleanupModule } from 'src/engine/core-modules/event-logs/cleanup/event-log-cleanup.module';
 import { FeatureFlagModule } from 'src/engine/core-modules/feature-flag/feature-flag.module';
@@ -58,7 +58,7 @@ import { AutomatedTriggerModule } from 'src/modules/workflow/workflow-trigger/au
     PublicDomainModule,
     EventLogCleanupModule,
     MarketplaceModule,
-    AppVersionCheckModule,
+    ApplicationUpgradeModule,
   ],
   providers: [
     DataSeedWorkspaceCommand,