[Apps] App misc - fixes + settings permissions for apps + uploadFile (#17167)

In this PR

- handle settings permission check for applications. Until then this was
unhandled and applications could not perform actions requiring settings
permissions, even if they were granted them

- fix ties to attachment, noteTarget etc: 
When an object had their fields synchronized in the app, the system
fields created as a side-effect of the object creation (relations to
noteTarget, attachment, taskTarget, favorites, timelineActivities -
created with `isCustom: true`, not sure that is correct btw) were then
deleted because they are not declared in the app, and identified as
deletable because of `isCustom: true`.
Updating the logic to exclude system fields from the logic that detects
fields to delete.
I think this outline the confusion we have around isCustom, isSystem
etc.

- introduce uploadFile util in generated twenty client as it cannot be
handled by the client's query / mutation. I had to use this for my
invoicing app

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

@@ -4,6 +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 { 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';
@@ -32,6 +33,10 @@ describe('PermissionsService', () => {
           provide: WorkspaceCacheService,
           useValue: {},
         },
+        {
+          provide: ApplicationService,
+          useValue: {},
+        },
       ],
     }).compile();