Merge branch 'release/2.2.9' into develop
Updated .gitigore to ignore the entire tmp/ and log/ folders.
Updated README to Markdown, adjusted formatting, and a few other details.
Removed TextMate project file.
Delete .DS_Store
Fixed README typo
Tweaks to the README
Update README.md
Remove migration files

that have any personal information in them
annotate models
Added dot files

to get application running locally
rename docs

renamed files and defaults that reference these files
1st pass at de-NUCATSification

Renamed NUCATS to NITRO ARM
next steps are to make values configurable
First pass at configuration

Most all NUCATS and NUBIC specific information can now be set per deployment
by editing the config/initializers/nucats_assist.rb file
Removed empty READEME file.
Added Jeff as admin
NucatsAssist module not loaded at this time
Sample sponsor setup
Remove reference to code in Gemfile

removed the source 'http://download.bioinformatics.northwestern.edu/gems'
and ran bundle update to ensure that all the gems can be retrieved from
https://rubygems.org or http://github.com/

Also added a database.yml.example file for those who are more familiar with
this type of Ruby on Rails setup (esp. new users adopting nucats_assist)
Fixes so that aker still works

There were two assumptions in the authorization steps
that a cookie would exist
and that the Aker::User was a User record

This commit fixes those problems