remove git submodules
Change all the dir structure to be used by stow.

* Move the different config files to their own dir: ruby, zsh, etc.
GIT: Add rbenv, ruby-build and vundle submodules
Add zsh prompt with git info.
Add scripts to checkm install and remove packages.
Update README and LICENSE files.
Install git submodules the right way.
Merge pull request #20 from jhbabon/refactor

Refactor