Fix buf v2 linting errors

During the migration we added the below exceptions to avoid larger changes at once. Remove the exceptions and fix linting errors where possible:
```
lint:
  use:
    - STANDARD
  except:
    - FIELD_NOT_REQUIRED
    - PACKAGE_NO_IMPORT_CYCLE
    - PACKAGE_DIRECTORY_MATCH
    - PACKAGE_VERSION_SUFFIX
    - SERVICE_SUFFIX
```

Some of these will be breaking changes