Adding biological scripts.

Most are from the Onuchic lab and are used for gromacs
Improved watchdropbox

Since it is run as a cron job, don't delete anything immediately after
copying. Instead, wait for the next invocation and delete it then,
when it has almost certainly finished copying.

Also, use hard links rather than a direct copy to save storage and time
watchdropbox accepts input files

* Fewer hard-coded paths
* Growl is now optional
Improving md_prep compatibility with PyMol 1.3
Better error handling in watchdropbox
Better error handling in solarized.sh for non-ubuntu
Improving install.sh comments & error handling
Adding solarized submodule
Switching back to cp for watchdropbox

Hard linking was preventing changes from being detected
ignoring solarized submodule