I do this all the time:
git add .
git add -A
git commit -am "foobar"
that adds everything so all of my changes are staged, but we have a git submodule in the config directory.
What I have been doing is using several of these commands to "get rid of changes to the config dir":
git reset -- config
git checkout -- config
git checkout origin/dev config
git reset HEAD config
Can anyone explain what these are doing? I am not even sure if the last command is doing what I think it does.