pre-commit hook question

Hello everyone. Im struggling for a couple of hours to make git store metadata of the files using metastore and I use hooks/pre-commit for this. The problem is that the script is invoked correctly, and modifies the file "metadata" but the file itself is not added into commit. I tried calling "git add metadata" and "git add -u metadata" but there is no effect. The file ends up uncommited and marked as modified or staged BUT not commited, ever.

Is there any way to make this work? Basically, I want it to update and commit the file "metadata" on each commit. (then i want to make the same on checkout, but first i need to make storing work correctly)

Thanks!

P.S. If you are wondering why I need this, the answer is I store OS files for an embedded device which needs permisions/suid flags etc.