Add maven plugin to assemble Jar with deps

Add maven-assembly-plugin to assamble jars with deps
to allow for easier distribution.
Add functionality for Permutations in rate Expressions

Permutations nPk=n!/(n-k)! are mathematical functions
that are requried as rate expressions in petri-nets
in some contexts.  Care is taken to avoid changing
existing code.
Merge branch 'stable-feature-perms' of github.com:maxf130/PIPE into stable-feature-perms