merged changes from trunk into new shell branch

.gitignore

CMakeLists.txt

build_configs/win32

cmake_support/FindFFTW.cmake

cmake_support/FindOPENSTRUCTURE.cmake

cmake_support/OST.cmake

deployment/linux/README.txt

deployment/linux/create_bundle.py

deployment/linux/create_qmean_bundle.py

deployment/linux/reset_repository.py

deployment/linux/reset_repository_qmean.py

doc/conf/conf.py

examples/dokk/KEYS

examples/dokk/config.py

examples/dokk/datafiles/dengue/level.ini

examples/dokk/datafiles/dengue/levelF.ini

examples/dokk/datafiles/dengue/ligand.sdf

examples/dokk/datafiles/dengue/protein.pdb

examples/dokk/datafiles/dengue/surface.face

examples/dokk/datafiles/dengue/surface.vert