Workflow and version control

The text editor in Studio strips comments and re-serializes (via the OWL API I imagine) and I can’t find any version control infrastructure. Any suggestions for workflow that preserves comments and controls the formatting of serialization for purposes of version control?

Maybe I should I stick with rdfs:comment for comments. That would address some of those issues. I reckon re-serialization is what makes #comments a problem anyway.

Does anyone use Protégé just to deal with diff and version control?

Anyone successfully using Tawny-OWL?