[permissions] Remove raw queries and restrict its usage (#12360)

Closes https://github.com/twentyhq/core-team-issues/issues/748

In the frame of the work on permissions we

- remove all raw queries possible to use repositories instead
- forbid usage workspaceDataSource.executeRawQueries()
- restrict usage of workspaceDataSource.query() to force developers to
pass on shouldBypassPermissionChecks to use it.

---------

Co-authored-by: greptile-apps[bot] <165735046+greptile-apps[bot]@users.noreply.github.com>

packages/twenty-server/src/engine/metadata-modules/remote-server/remote-server.service.ts

@@ -271,6 +271,7 @@ export class RemoteServerService<T extends RemoteServerType> {
     const [parameters, rawQuery] =
       buildUpdateRemoteServerRawQuery(remoteServerToUpdate);
 
+    // TO DO: executeRawQuery is deprecated and will throw
     const updateResult = await this.workspaceDataSourceService.executeRawQuery(
       rawQuery,
       parameters,