[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/guards/settings-permission.guard.ts

@@ -8,8 +8,8 @@ import {
 import { GqlExecutionContext } from '@nestjs/graphql';
 
 import { msg } from '@lingui/core/macro';
-import { WorkspaceActivationStatus } from 'twenty-shared/workspace';
 import { type PermissionFlagType } from 'twenty-shared/constants';
+import { WorkspaceActivationStatus } from 'twenty-shared/workspace';
 
 import {
   PermissionsException,
@@ -47,6 +47,7 @@ export const SettingsPermissionGuard = (
           setting: requiredPermission,
           workspaceId,
           apiKeyId: ctx.getContext().req.apiKey?.id,
+          applicationId: ctx.getContext().req.application?.id,
         });
 
       if (hasPermission === true) {