updated scons and beast config

- add multiple target rule for running beast from scons.
- remove log file prefix code from mkbeast.py b/c beast has an option to
  to prefix log files.
- enable per-patient monophyly restrictions in constructed beast
  config.  This means beast will fail b/c initial state is incompatible with
  hard constraints, but will solve that next by precomputing a starting tree.