modify apache site configuration to prevent direct access to non-API PHP files

* also made some changes to the apache log checker to grep out known-harmless things so the logs will be easier for me to read (mentioned in #627)
* Fixes #626
* Jenkins: http://jenkins.buttonweavers.com:8080/job/buttonmen-cgolubi1/185/
* needs to be tested using vagrant if you want to test, since the change is a change to apache config which is only managed under vagrant