Updating README

Fixing spellings & adding git submodule commands
Removing ulimit from bashrc

Process limits apply globally on ubuntu (BAD!)
Updating synergy.conf for my current layout
Adding global .cvsignore file

It currently ignores vim recovery files in git, cvs, rsync, etc
[ENHYDRA] Adding script to switch gnome terminals to solarized
Ignoring a vim history file
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.
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