source-tests.sh: Improve source checks

This are two changes in one:
* When running make check, check all changes that are not
  yet commited.
* In pre-commit hook, only run on the files in the staging area,
  eg, the ones that are going to be commited
* Filter out deleted files from list of files that are changed,
  otherwise you cannot delete files.
* Avoid a grep, do the filtering in git-ls-files.

Change-Id: I312c4b21bf9a009bf140b8eebc4eabb6ed3cfc7e