Fix bugs introduced by lint

Revert the change introduced by my lint cleanup that probably broke the Python and MATLAB wrappers: changing "using namespace caffe" to "namespace caffe { <entire wrapper> }".  Sorry!

@shelhamer, could you check that this resolves the issues you were having with the Python wrapper? When I diff the versions of the wrappers in this PR against bca6595 (which @shelhamer reported as working), I now see only style changes that I don't think could alter any behavior, with the exception of changing the single-argument CaffeBlob constructor to be "explicit" in the Python wrapper.  (At some point it would be nice to have a couple small unit tests for the wrappers, at least to check that they run at all.)

Also slipping in Makefile changes to suppress unnecessary output ("Done processing...") and not rerun lint if successful and no source files have changed.