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


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packages/twenty-server/src/engine/core-modules/logic-function/logic-function-drivers/drivers/lambda.driver.ts

@@ -38,7 +38,7 @@ import {
   LogicFunctionExceptionCode,
 } from 'src/engine/metadata-modules/logic-function/logic-function.exception';
 import { type FlatLogicFunction } from 'src/engine/metadata-modules/logic-function/types/flat-logic-function.type';
-import { copyYarnEngineAndBuildDependencies } from 'src/engine/core-modules/application/utils/copy-yarn-engine-and-build-dependencies';
+import { copyYarnEngineAndBuildDependencies } from 'src/engine/core-modules/application/application-package/utils/copy-yarn-engine-and-build-dependencies';
 import { type LogicFunctionResourceService } from 'src/engine/core-modules/logic-function/logic-function-resource/logic-function-resource.service';
 import { callWithTimeout } from 'src/engine/core-modules/logic-function/logic-function-drivers/utils/call-with-timeout';
 

packages/twenty-server/src/engine/core-modules/logic-function/logic-function-drivers/drivers/local.driver.ts

@@ -14,7 +14,7 @@ import { ConsoleListener } from 'src/engine/core-modules/logic-function/logic-fu
 import { TemporaryDirManager } from 'src/engine/core-modules/logic-function/logic-function-drivers/utils/temporary-dir-manager';
 import { HANDLER_NAME_REGEX } from 'src/engine/metadata-modules/logic-function/constants/handler.contant';
 import { LogicFunctionExecutionStatus } from 'src/engine/metadata-modules/logic-function/dtos/logic-function-execution-result.dto';
-import { copyYarnEngineAndBuildDependencies } from 'src/engine/core-modules/application/utils/copy-yarn-engine-and-build-dependencies';
+import { copyYarnEngineAndBuildDependencies } from 'src/engine/core-modules/application/application-package/utils/copy-yarn-engine-and-build-dependencies';
 import type { LogicFunctionResourceService } from 'src/engine/core-modules/logic-function/logic-function-resource/logic-function-resource.service';
 
 export interface LocalDriverOptions {