Add gem-friendly directory structure.

To push out gem versions of MesaScript, created mesa_script directory, which
largely just contains copies of original files in a rubygems-friendly structure.
The new mesa_script.gemspec file contains the metadata and instructions for
building the gem, which is now hosted.
Update documentation for recent changes.

Now documentation reflects how multi-dimensional arrays are handled and also
shows how the newly-made `unflag_command` method works to unflag inlist commands.
Remove redundant files.

After the move to a rubygems-friendly file structure, removed unnecessary source
files at the root level. Retained copy of README for convenience on the github
page.