Sorts the QM files into seperate folders by method

Currently, if you keep a standard folder and change the method used from pm3 to pm6 (as an example), you may be using old pm3 calculations when you intend to use pm6. These changes create a new subfolder, named after the method, within your QM folder. In the case that someone would want to use old pm3 calculations but run new ones at pm6, they could copy the pm3 files to a pm6 folder. This avoids overwriting possibly useful files that used a different method.

Additionally this also contains some changes to the logging messages and storing of the qm thermo data. We weren't storing comments about where the thermo data came from when using Gaussian, but we also weren't logging some thing on the MOPAC side. Things should now be consistent.