1. some code cleanup
2. Finished integration of BFGS method for simultaneous optimization
   of GTR rate parameters. It will only be invoked on single-partition DNA
   datasets, because a version for several partitions requires substantially
   more work, since paremeters for all partitions need to be changed simultaneously
   following the approach described here: http://sco.h-its.org/exelixis/pubs/ICPP2009.pdf

   Performance-wise I observed a speed improvement of up to 32% for optimizing model params & br-lens
   on a fixed single-gene tree with 2554 taxa

3. To disable BFGS optimization in case of bugs I added a new flag --no-bfgs to disable bfgs
   optimization.