[MACOSX] Adding ruby environment manager path
Ignoring .DS_Store globally
[MACOSX] Adding FileMerge as git difftool
Ignoring .DS_Store globally
Adding md_prep pymol script

Used to prepare structures to send to gromacs via the dynamics plugin.

Current goals are better hydrogen generation and MSE substitution
Fixing solarized.sh script
Adding bin for scripts, with new run_on_update script

run_on_update watches a file for updates and runs a command after
modifications.

Also moved solarized.sh into the bin folder
Extended run_on_update to watch multiple files
Rewrote md_prep.py.

The rename_h function works for standard AAs, although it could
use more testing.

The script requires the geo module from geometry-simple.
Merge branch 'master' into isabelle

Some commits were previously cherry picked into master,
but the merge introduces several changes picked from enhydra.
Adding general scripts

* Progress bars:
  * bar - Use like `cat`
  * progressbar.sh
* diffshallow - quick recursive directory diff
* kenken.py - calculate kenken possibilities
* synergyc_secure - synergyc through an ssh tunnel
Merge branch 'master' into isabelle
[MACOSX] Adding isabelle scripts

* checkservers - check that servers are running
* watchdropbox - check if anything new has been added to dropbox
* trash - delete things using Finder rather than rm (Keith Beckman, GPL2)
* ignore some one-off installs that want to live here
Adding biological scripts.

Most are from the Onuchic lab and are used for gromacs
Adding obsolete stikkit archiver
Removing obsolete stikkit archiver