Added the JEX and Workflow class.

git-svn-id: svn+sshtunnel://coge.iplantcollaborative.org/storage/SVN.d/CoGe@949 aead6680-5d07-0410-860c-d65e5a4cd256
Individual Feature Tracks can now be zoomed out much further


git-svn-id: svn+sshtunnel://coge.iplantcollaborative.org/storage/SVN.d/CoGe@950 aead6680-5d07-0410-860c-d65e5a4cd256
Implemented base functionality of JEX module.
Moved the Workflow to its own seperate module.
Added connection string and port to JEX.
Connection string now takes a host, port and returns the connection string.
Cleaned up get_status.

The get_status method does not print to stdout any more.
An additional fail status has been added when a makeflow has failed.
Refactored add_job for a cleaner implementation.
Added filepath option for workflow files.
Polling for complete is now more aggressive.
Added ability for workflow to choose a log file.