Unable to track files within Git submodules

Question

Problem: to add files at ./shells/smallApps/* to Git at ./.git/ when I do not have the files at ./.git/info/exclude n

Answer 1

I see you've got git add saying something about submodules. Do you have nested Git repositories? Do this:

$ find . -name .git

How many .git directories are listed? If there is more than one, then you've got multiple nested repositories and that could be a cause of some of this confusion.