Documentation fixes, new CUDA_PROPAGATE_HOST_FLAGS, changed output di…

…rectory.

- Finished updating and formatting documentation.
- Added CUDA_PROPAGATE_HOST_FLAGS (Default ON) that can disable the C flag
propagation to the host compiler.
_ Changed the output directory for support files from
${CMAKE_CURRENT_BINARY_DIR} to ${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles.  This
will hopefully reduce the clutter in the binary directory.