Add Makefile.
Refresh.
Add/fix documentation.
Move toolshed config files onto the tools volume.
Save/restore volume directory skeletons.
Add a few dependencies to the makefile.
Decrease duplication and reconfigure volumes.

The startup scripts are now broken into two: docker-cmd.sh, which does
basic runtime configuration, and startup.sh, which is actually
responsible for starting the Galaxy server(s).

I also reconfigured volumes, again. It's a lot nicer to have a single
export directory that docker-cmd.sh can migrate data to, and the
environment variable GALAXY_EXPORTS defines what directories get
exported.