Update manifest structure (#17547)

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

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

packages/twenty-front/src/generated/graphql.ts

@@ -271,7 +271,7 @@ export type Application = {
   applicationVariables: Array<ApplicationVariable>;
   canBeUninstalled: Scalars['Boolean'];
   defaultLogicFunctionRole?: Maybe<Role>;
-  defaultLogicFunctionRoleId?: Maybe<Scalars['String']>;
+  defaultRoleId?: Maybe<Scalars['String']>;
   description: Scalars['String'];
   id: Scalars['UUID'];
   logicFunctions: Array<LogicFunction>;