Reorganize repo as a single image.

Both the single- and multi-process servers can be launched from this
image by calling a different startup script. docker-entrypoint.sh
performs common configuration steps, and the startup-*.sh reconfigure as
necessary to run the requested setup.

Squashed commit of the following:

commit 665efc5aaa05f5cb34af8cd0925c5fdf50cb8e73
Author: Brian Claywell <bclaywel@fhcrc.org>
Date:   Fri Jul 25 21:18:31 2014 -0700

    [WIP] Add some comments.

commit 5ce497b3260b3cef89c6e159aea0cf0d740b2815
Author: Brian Claywell <bclaywel@fhcrc.org>
Date:   Fri Jul 25 21:10:02 2014 -0700

    [WIP] Switch to ENTRYPOINT and fixups.

commit 645efcb4779e8f44804079502c97a379a6f7f7a7
Author: Brian Claywell <bclaywel@fhcrc.org>
Date:   Fri Jul 25 20:15:03 2014 -0700

    [WIP] Reorganize for single image.
Add private/ directory.
Return code on error.
Add support for an ssh key.
Generalize ssh configuration.
Start the proxy later.
Add a few minor comments.
Add handling for private job_conf.xml.
... and be a little noisy about it.
Give startup scripts better names.
Rework and cleanup startup-custom.sh.
Switch to absolute paths for toolshed options.
Refresh.
Trying relative paths again.
Relocate datatypes_conf.xml.
Export display_applications directory.
Generalize exports.
Rename export variable and add check for /export.
Pull out data export script for reuse elsewhere.
Remove hardcoded exports.