Use absolute include paths in nbnxn kernels

Currently, the WIP automatic include sorter expects these files to be
included as paths relative to src/, and so does doc-check after changes
done for the include sorter.  Change the generator source files to
account for this, and regenerate the kernels.  Can be improved in the
future.

Make the kernel generator work even if the current working directory is
not the same as the script directory.

Change-Id: Ibc603dd0c85291f0c8fede394d9fa35b39c3a0a4