adding .conf to file checks
explicitly say to create the a2* modscripts
specified default should be 000-default because otherwise the a2* scripts in ubuntu/debian will not know what to do
allowing for .conf sites as well as sites with no extentions
adding .conf on to default site
adding - before ExecCGI
changing that to a plus
Merge pull request #148 from drpebcak/COOK-3900

Fixes for #142 and #146