Remove old dead test/prototype code
Close all of the runnable externals
Add more javadocs
Add a test for the jetty server
Merge pull request #10 from areese/cleanup_tests

Cleanup tests
Cleanup the building of directory names in preperation to remove the whole ROOT hack and replace it with something else
Merge pull request #11 from areese/fix_root_mess

Cleanup the building of directory names in preperation to remove the who...