Uncrustify all files

Add a script that can be used to do this again if necessary.  The script
also supports listing the files based on the filter attribute, and
checking the copyright; can be extended if/when there is need.

Some manual reformatting in gpu_utils.cu, nbnxn_cuda_data_mgmt.cu, and
nbnxn_cuda_kernel.cuh.  Updated the Sparc kernel generator to generate
code that is invariant under uncrustify, like the other kernels already
do.

Copyright not updated, except for fixing readpull.c such that the script
doesn't complain.

Part of #845

Change-Id: Ia77738ec781f75f1c4e7a264734aac884321f3e5