TIL: Discover Why Git Won't Track a File
This was frustrating. I couldn't track changes to multiple files buried in a folder!
Again, Stack Overflow to the rescue. Use git check-ignore -v <filename> to see why your changes are being ignored.
git check-ignore -v plugins/myfolder
This should spit a .gitignore filepath, or some other reason why your file has been ignored. In my case, it even worked with a broken submodule, which was the root cause I couldn't track/commit changes.
PS. Turns out this awesome fellow, after initially answering the question with a "Nope, sorry, not supported" wrote git check-ignore to support this functionality. Where else do you get such help?