Adding a submit scripts directory.

This should house template scripts for different clusters.
Updating scripts.

Updating the setup repoistories script to name directories correctly,
and get the MPAS-Scratch repository as well.

Adding a sync_mpas_repositories script that syncronizes remotes for each
of the MPAS repositories. (Makes sure they exist, and adds any new ones)

sync_mpas_repositories.sh assumes your directory structure was setup
with setup_mpas_repository.sh.
Changes for my preferences
Some changes to git settings for my preferences
Changes configuring for cluster.
Changes to hopefully make the dot files compatible with mac
Fixed vi vim aliasing issue.
bug fix
bug fix
Fixes issue with color-coded grep
Fixed the general issue of potentially aliasing grep, etc for color
support.
Added ability to restore deleted files
Changes corresponding to setup for MacOSX.
Fixed rainbow parentheses
Added backup for spell checker for vim
Changes to spellfile
Changes to write spelling file
updated spelling list
spell bug
Added support for tab key mappings in vimrc