ENH: Check that git directory is writeable

and avoid undefined index usage if it's not.
BUG: Fix undefined variable usage in changes viewer

This commit fixes the following error:

  PHP Notice:  Undefined index: checkindate in /var/www/cdash/viewChanges.php
   on line 355
BUG: Overhaul configure warning extraction algorithm

This fixes warnings duplication and makes extraction actually work
(even with autotools projects).