Suddenly, when I should commit to my repo, the .spans and .ecodiag files are named with GUIDs instead of the more readable filenames they used to have.  

Is this behaviour expected? Why do I suddenly have these? 

This is an old setting in the modlr settings file: modlr.config

Clear the PreserveLegacyFilenames to empty or false (at some point when saving, someone said yes to the question to PreserveLegacyFilenames).