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.
Fix docker-clean target.
Add clean target.
Clean up after ourselves a bit more.
Explicitly setting HOME fixes the egg cache error.
Disable multiple web processes.

There's an issue with administrative tools when there's more than one
web process; with two, one of the processes appeared to have
toolshed-installed tools available, while the other reported errors
about the tools not being installed.