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Set nonbondThreadsPerBlock to gpu->sim.nonbond_threads_per_block

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M    amoebaCudaGpu.cpp
M    kCalculateAmoebaCudaMapTorques.cu
M    kCalculateAmoebaCudaRotateFrame.cu

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M    AmoebaMultipoleForceImpl.cpp

Updated build script to require CMake 2.8, since CMAKE_OSX_DEPLOYMENT_TARGET is not supported on 2.6.

Change doctests to reflect better preservation of tuples in collections of collections.
Note that outer container is still converted to list...