Issue #39. Reduced number of overlaps recorded that would get ignored later.

I'd also assumed that all plugins listed would exist, forgetting that
BOSS just adds error messages and doesn't fail at that stage, so added
checks for that. Also figured out why adding edges to the graph was
crashing: it doesn't seem to like connecting to the last vertex in the
graph. Haven't figured out where I'm going wrong beyond that though.
Issue #39. Added saving of the graph for visualisation purposes.

Still haven't figured out that crash bug.