Apply clang-format-all.sh using the _clang-format file through all the cpp/.h files.
make sure not to apply it to certain serialization structures, since some parser expects the * as part of the name, instead of type.
This commit contains no other changes aside from adding and applying clang-format-all.sh
fixed some more warnings
added alignment macros to some classes
btPersistentManifold from 128 to 16 bytes aligned
prepare command to select collision filter mode (SIM_PARAM_UPDATE_COLLISION_FILTER_MODE)
