RSA interface should ensure external reference

[laroque]

Should be easy to do, the start_run process already sends a bunch of commands at the RSA. The change is to simply add a step which checks if the current reference state is set to "external" or "internal" and, in the latter case, raises an error telling the user to fix the reference first.

It would also be good if the run command had an optional argument (default to false) which, if true, would skip this check. That way we can run without the external reference check if we want/need to do so, but would have to actively opt-out each time. (Forcing to do it each time rather than setting a property to disable it is desirable since in the latter case you could forget to turn it back on and still screw yourself).

[laroque]

This issue is now part of dragonfly so I'm moving it to issue #5 there