I'm running Node 6.3.0 on a MackBook I just set up running OS X 10.11
I installed Node using Homebrew and I noticed that when I run
npm install gulp --save
You are probably using an older version of npm (< 3) on your Linux box. With npm 3 they changed the way they store dependencies and try to flatten the dependencies tree. e.g. If you had a project A that requires B and that requiring B it would look like this:
Hope this helps.