So, for fun, I made a file and marked it, then deleted it. I also manually edited the .cfg.json to see what that was all about.
Currently, the error message is just:
drake@element:~/workspace/test_base$ cfg snap checkout master
error: there are uncommitted files
'git status -s' output:
M .cfg.json
D .cfg_schemas/lol
D lol/hh/lol.yaml
I think that the error message seems somewhat... barebones. Could be nice to update this to be more consistent with cfg / suggest how to fix the issues with modified / deleted, but it just feels weird to show a git message here.