Update and cleanup core commit code

Update and cleanup core commit code

It's time to update this very old part of code.

Problem is that it still relies on plumbing git commands
as 'git update-index' or 'git read-tree'.

This patch restructures the commit code to use newer and
officialy suggested 'git add', 'git rm' and 'git reset'
to update the index with the paths to commit.

As a side effect the code is much more clean now.

Signed-off-by: Marco Costalba <mcostalba@gmail.com>