Because story files are HTML files, they can be tracked using source control software like Git. If you do track story files in source control, quit Twine before taking any actions that will cause the story files in your library to change, like pulling from a remote or merging branches.
Twine compresses the HTML of story files, which can make reading diffs of stories difficult. Converting your stories to the plain-text Twee format before checking them into a source code repository can help with this. Command-line tools like Tweego, Extwee, and twine-utils can do this for you.