Load and save junctioned source refs from/to junction.refs

  o _projectrefs.py: Additional constructor option to choose the base name

  o _project.py: Load two ProjectRefs objects, one for the junctions

  o source.py: Load and save junctioned source refs with the appropriate ProjectRefs object

  o tests: Updated some tests to expect junctions to be stored in junction.refs

This fixes issue #361