[DAEMON-221] gulp upgrade: Run 'yarn' in top-level after updates and 'yarn upgrade' for each package

The gulp upgrade task does a good job of updating all of the npm dependencies in each package's package.json, but the top-level doesn't actually install the new deps. I think we simply need to remove the call to lerna bootstrap and call yarn. Also, we never upgrade the dependencies of dependencies. We need to write temporary package.json files with no appcd-* deps, run yarn upgrade, then restore the original package.json. This will update the yarn.lock files.