cygwin, 44k files: how to commit only index?

I have a kind of awkward project to work with (~44k files, many binaries).

The normal "git commit", which seem to be more than enough
for anything and anyone else, is a really annoying procedure
in my context. It spend too much time refreshing index and
generating list of the files for the commit message.

At first I stopped using git commit -a (doing only update-index),
now I'm about to start using write-tree/commit-tree/update-ref
directly. It helps, but sometimes I really miss -F/-C. It's also
ugly: I can (and almost did) commit an unchanged tree.

Is there any simple way to modify git commit for such a workflow?
Failing that, any simple and _fast_ way to find out if the index