On fish 3.1.0, Linux Mint 18.3 via the ppa:fish-shell/release-3 .
When I try to git add files with changes, fish doesn't do it, see this example where I try to add a file and git add only sees some unrelated untracked files:
https://asciinema.org/a/a4mpxoO8I0ok2wBYlQoj9JK2v
I played around with different config.fish, completions/git.fish etc., nothing helped. When I downgrade to 3.0.2-1511-gd903fe6 (randomly chosen because this is the version I use on a cluster), everything works as expected.
This is probably related to #5648 only for 3.1.0