Update manifest structure (#17547)

Move all sync entities in an `entities` key. Rename functions to
logicFunctions

```json
{
  application: {
    ...
  },
  entities: {
    objects: [],
    logicFunctions: [],
    ...
  }
}
```

packages/twenty-server/src/engine/api/common/common-query-runners/common-base-query-runner.service.ts

@@ -319,8 +319,8 @@ export abstract class CommonBaseQueryRunnerService<
       );
     }
 
-    if (isDefined(authContext.application?.defaultLogicFunctionRoleId)) {
-      return authContext.application?.defaultLogicFunctionRoleId;
+    if (isDefined(authContext.application?.defaultRoleId)) {
+      return authContext.application?.defaultRoleId;
     }
 
     if (!isDefined(authContext.userWorkspaceId)) {