I don't understand why you need this as a hook. In recent versions of git, "git add" on a directory updates the index to match the entire directory, with modifications, additions, and deletions.
README.txt
src/
include/
doc/
TODO.oo3
I don't want to "git add" on the project directory, or any of the subdirectories other than TODO.oo3 because I don't want to pick up those files. For everywhere except TODO.oo3, "git add -u" is what I (think I) want. It's only with TODO.oo3 that I want "git add" instead of (or in addition to) "git add -u".
I mostly use "git add -p" and it misses new files, which doesn't feel right either :\