Here are the apparently not-so-simple requirements:

1. GitHub shorthand syntax (org/repo) should be handled the same way by the CLI, regardless of whether it's passed in via the command line, or edited into package.json.
2. --save, --save-dev, and --save-optional should save GitHub dependencies as shorthand syntax, and not normalized to git+whatever: URLs, so that the symmetry of using them is preserved between the first and subsequent times you install them (shrinkwrapped GitHub dependencies should continue to resolve to git+x: URLs + resolved commit hashes).
3. Explicit Git URLs pointing to GitHub repos should preserve the protocol that was provided either on the command line or in package.json.
4. Explicit Git URLs pointing elsewhere should also be left alone, whether passed in on the command line, or via package.json.

We've made a few passes at this, which can be seen in #2556, #6978, #7121, #7486, #7630, #7766, and #7829. It's time to nail this down once and for all, and to get the right set of tests around it to prevent it from regressing in the future (although that is proving to be hard to do).