Expand repertoires only to Subsystem nodes
Make cut an attribute of Subsystem
Default to null_cut, fix typo
Remove cut parameter in Concept.expand_repertoire
Update examples to use new Subsystem signature
Accept cut == None in utils.apply_cut
Fix order of current and past state
Condition and cut in Subsystem init, not in C/E

- Cuts are now applied at the subsystem level.
- Move the logic for conditioning on external nodes and applying the cut
  outside of the cause/effect repertoire functions.
- Subsystem now has a past_tpm and a current_tpm: these are the
  network's TPMs, but conditioned on the past and current states of the
  nodes external to the subsystem.
- The Subsystem also has a connectivity matrix, which is the network
  connectivity matrix with the cut applied and the external nodes cut
  off from any internal nodes.
- This simplifies the C/E repertoire calculations, and Node
  initialization.
- Nodes now have a past and current TPM as well.
- Nodes only need to modify the Subsystem's TPM by marginalizing
  non-input nodes *within* the subsystem to get their own TPM.
Fix Subsystem.indices2nodes
Remove obsolete C/E rep. validation test
BUG: Fix node TPM marginalization
Update compute to new Subsystem signature
Return BigMip regardless of Phi value
Only compare node indices in Subsystem eq
Cut subsystems must share the MICE cache of the uncut one
BUG: Use the constellations of the *cut* subsystems!
Cuts are now indices, not nodes
BUG: Use node indices as keys in mice_cache to avoid catch-22 when pickling
Default to null cut in Subsystem
utils.apply_cut takes cuts with indices rather than nodes