BigMerge, finally

Finally able to push all my work from the last few days to master. My previous branch got completely messed up for some reason and had a million conflicts and was 30 some commits ahead and behind and it was a mess. So I made a new branch, put all my work there, and now I'm good to go. As far as the work:

Parse.py
> Worked on parse.py, added support for MATLAB, block python comments, and some other stuff
> Added function to check for user-supplied flags to go alonside our check for default flags
> Added declaration for the final function in parse.py that I think will be mainly responsible for performing all the checks and relaying the nicely structured onto Jasons database.py. I have a lot of notes and thinking-out-loud in there so you guys should take a look and let me know what you think

parse_test.py
> This is where all 20 unit-tests that I've written so far are. They test succesful calling of a few functions from the command line using subprocess, they test check_comment_line, check_for_default_flag, and check_empty and so far all those 20 tests pass perfectly. So with what I have to this point as far as tested functions, we are golden. I will continute to work on unit tests for more functions in parse.py
> As far as overall testing framework, nosetests is what I'm using for the moment to run all the tests in parse_test.py. I will work on figuring out tox and getting that to work smoothly in the upcoming days