Update manifest structure (#17547)

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

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

packages/twenty-sdk/scripts/generateBarrels.ts

@@ -33,7 +33,7 @@ const EXCLUDED_DIRECTORIES = [
   '**/internal/**',
   '**/cli/**',
 ] as const;
-const ROOT_DIRECTORIES = ['application'];
+const ROOT_DIRECTORIES = ['sdk'];
 
 const prettierConfigFile = prettier.resolveConfigFile();
 if (prettierConfigFile == null) {