Merge changes from colinDev

[bentsherman]

These changes look pretty good, I really like the flags for running individual algorithms. A few small things:

• You copied the include files into include but they aren't used anywhere yet, so you should either go ahead and delete the copies in src and update the makefile and whatnot or delete the include folder. Honestly right now I'd rather leave everything in src until you can lay out a better plan for organizing the source files.
• There are two lines in db_train (the calls to m_copy) that were commented out but now they're uncommented, I was using them as a quick and dirty way to short-circuit LDA and ICA so they can be deleted now.
• This one's up to you, but your clean-home.sh script could be incorporated into the Makefile under make clean since it's pretty similar.

Anyway, let me know what you want to do with this include folder and then we can merge.

[ctargon]

I say delete the Include folder since there isn't a solid way to incorporate it yet. Other than that, it seems good to merge now. When I get home I will look at that clean script and see what can be done. Also, I think the cross-validate.sh script might need some work to incorporate the flags. I haven't tested that very thoroughly yet.