Prompt to confirm when installing a bundled package

[kevinsawicki]

For some reason there are many reports of people installing bundled packages explicitly with apm install.

The initial idea was to allow this in case someone wanted to explicitly manage their version or install a new version before the next Atom release is out.

The problem is that sometimes due to Chrome/Node upgrades or API changes, versions aren't compatible anymore.

Therefore going forward, tell people when installing a bundled package, that this package comes with Atom, and make them confirm that they really want to install it.