Discard phase points in *-segregate-phases if absent from SVM model

This fixes #3.

If no samples have been taken at a phase point, the SVM model will not
know about it can thus no graph edges will connect to that point.
Previously, those points would still be included in the graph analysis,
resulting potentially in many disconnected points and a large degeneracy
of eigenvalue zero. The new behavior is to discard those phase points
flat out.