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/nest-cli.json

@@ -21,11 +21,11 @@
         "outDir": "dist/assets"
       },
       {
-        "include": "engine/core-modules/application/constants/seed-dependencies/**",
+        "include": "engine/core-modules/application/application-package/constants/seed-dependencies/**",
         "outDir": "dist/assets"
       },
       {
-        "include": "engine/core-modules/application/constants/yarn-engine/**",
+        "include": "engine/core-modules/application/application-package/constants/yarn-engine/**",
         "outDir": "dist/assets"
       },
       {