Cleaned up code and made compatible with pancancer_bag changes

I have made several changes, deleted / cleaned up lots of code. Currently bindle is able to install multiple seqware workflows by providing a comma separated list in the bindle config file. I have also made changes to pancancer_bag that makes it so that ansible installs the workflows. I will be pushing the pancancer_bag code next. 
Check this, I don't see new sample bindle config files in the template folder.