andrewrutter there is a desktop beta version available on the forums that allows for saving projects as a folder of files instead of a single file. Some users using this with version control tools like git and SVN. In terms of versioning this obviously works fairly well, but some project level changes can touch on a lot of files, and merging such changes could cause conflicts. I haven't tried using this myself to comment on how much of an issue it is.
This idea has previously been suggested here, and we have given an official response.