Refactoring review

(PR based on PR#159)
I've started to review the changes we made in the refactoring process. 
I made some corrections/cleaning and start documenting a little. I tried to move the existing documentation in the source files as we discussed to have clearer header files. I did that for most of the files in medCore, except the ones Flo is exploding.
There is still a lot to be done. If someone wants to take over, please don't hesitate ;), otherwise, I'll continue when I'm back in 2 weeks.