Add option to control intermediate dumping in BackrubProtocol

[roccomoretti]

Especially with XML (where the Backrub protocol is part of a more extensive protocol), you don't necessarily want an unconditional dumping of the last & low results from the Backrub stage. This PR adds an XML option which will allow the dumping of the poses (old behavior), but turns it off by default. This only changes XML usage -- I didn't change how the backrub application behaves.

Changes to the backrub_interface_ddG integration test is expected.