Add more documentation on configuring server, etc....

Also reorganize to down play legacy job runner configurations.
Add some initial dependency documentation. Need to add a lot more.
Improved LWR dependency resolution.

WARNING: If you were using remote dependency_resolution on the Galaxy side, you will need to update to the latest Galaxy client since the dependency resolution contract interface has been reworked. I try not to break backward compatibility like this - but I had not reports of people using this functionality.

This changeset allow the client to pass more information needed about the tool's dependency context to resolve tool shed dependencies correctly.
Allow specification of SSL client authentication parameters to the kombu
connection. This is done via the `amqp_connect_ssl_*` options in `server.ini`.