Adding an API proto file, file gets deleted by `proto_format`

Following the instructions from [STYLE.md](https://sourcegraph.com/github.com/envoyproxy/envoy/-/blob/api/STYLE.md), step 4 suggests your new file will be automatically included in `api/versioning/BUILD`, but in fact, with the current implementation, if you don't add it manually, your new file will be deleted by `proto_format.sh fix`

Either the doc should be updated to match reality, or (preferably) the behavior should be updated to match what it used to do with one fewer manual step.