Reorganizing database structure so Github repo is inside project directory.

It took some work, but it turns out that the changes required to the current repo are very minor. This checkin is meant as a first step in the process of reorganizing the directories. It basically allows you to reorganize using the config file, and leave the current repo in its own directory with very few modifications. I have found already that it is much easier to work this way.

Most of the changes are bug fixes or small enhancements that were necessary anyways. Most of the work was already done by the various pointers inside the config file.

See the new configuration.inc.github.php file for directions on how to set it up.

Future changes to complete the process will include:
- change some of the hard-code pointers in the various index.php and qcubed.inc.php files
- change the use of __QCUBED__ in the autoloader, which may change anyways with composer
- create an installer to move things around so user doesn't have to.