Suddenly, when I should commit to my repo the .spans and .ecodiag files are named with guids instead of the more readable filenames they use to have. Is this expected behaviour, or 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 you someone said yes to the question to PreserveLegacyFilenames)