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