add spire dependency
Merge branch 'master' into spire
skeletal new-style spire process
sketch of a new state
compiles, anyways...
add multiset!
minimal regression for

  java.lang.ClassCastException: [Ljava.lang.Object; cannot be cast to [I

when trying to dereference a State
fixed issue with StateBuilders
our new requirement is to insist on initialising the model before
touching any variables. fix, for now.

remove reference in automatic models to the Kick model until we
put back a way to do partial derivatives
rejigg tsvhandler to apply a predictable ordering
test tsv handler complete output
re-arrange naive scheduler test to do initialisation in correct order
calculate total energy on initialisation and not during declaration
python process tests need to do initialisation
correctly propagate only child variables, and remember to actually run
the child process
cosmetic, pretty printing
slightly loosen rules for adding duplicate indices
fix initialisation ordering
correct, working reaction networks. still missing equality on
multisets, and in particular MassActionReaction
remove excessive explicit copying of different datatypes