[WIP] Updated vagrant scripts for conda build and upload

It appears that were lots of deadlinks that appeared in our old vagrant scripts.  I believe the current scripts should work out of the box for building the 6.1 release.  

I have uploaded a 6.1 Linux conda package here: https://binstar.org/omnia/openmm/6.1/download/linux-64/openmm-6.1-py27_0.tar.bz2
WFIW, you can change this to `Miniconda-latest-Linux-x86_64.sh`, to avoid having to update the version.