git ignoring a directory, it's like it doesn't exist

I have no idea what the problem was or how it arose (v. annoying), but here is how I fixed it, in case anyone else gets stuck:

git rm --cached a/b/c
git commit -m "removed phantom a/b/c dir"
git add a/b/c
git commit -m "finally able to add a/b/c"

Interestingly git log a/b/c only lists the "finally able..." commit. git show HEAD^ (the "removed phantom..." commit says

-Subproject commit c311ccdc91c8be66019aa138d1c4af49a6b7a81c

So it looks like it was treating it specially some how. I'm going to have to read up more on subprojects and/or submodules.

Do you have a global gitignore file ? (Check with git config core.excludesfile)