argpase instead of docopt
argparsing should work
releasing GIL fix #35
Executors: LinearSequenceExecutor (old behaviour), PhaseExecutor (specify phases to execute), ParallelExecutor
SWIG with thread does not work.

Other changes:

* executing sofa catches output
* change in exporter behaviour (exporter should not update the memory, just return an update)
* log.py is thread safe (maybe this helps markus)
Merge branch 'master' into executor_rework
Merge branch 'argparse' into executor_rework
Bunny works with phase and linearexecutor
simplified interface for defining exporters
Fixed bug in MiscMeshOperators (VTK 5 compatibility), please use the provided __SetInput functionality.
Patched simulation_runner to support new phase executor
fix #119
Merge remote-tracking branch 'origin/master'
Merge branch 'master' of github.com:CognitionGuidedSurgery/msml into febioExporter
unit test for c++
add circle
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