Merge pull request #240 from jeffdonahue/rm-cuda-kernel-loop-comments

Fix minor issues related to CUDA_KERNEL_LOOP -- merging myself as I'm only adding/removing comments other than the addition of CUDA_KERNEL_LOOP to PaddingLayer (and checked that this passes all tests).
add libcaffe.a to TEST_ALL_BIN dependencies in Makefile
also fix for runtest