chore(npm): don't clean npm-shrinkwrap.json instead generate npm-shrinkwrap.clean.json

Previously we would clean up npm-shrinkwarp.json file in order to achieve serialization
stability, which would then allow us to create human readable diffs that allow code reviews
of npm-shrinkwrap to be meaningful.

This cleanup process does have an impact on the functionality of npm which was only recently
discovered by Vojta, when we tried to update to new Karma version. See: socketio/engine.io-client#370

According to Julie, the root cause of these issues is npm/npm/#3581.

The workaround implemented in this commit is not to interfere with npm-shrinkwrap.json file, but instead
preserve the cleaned up version of its content in npm-shrinkwrap.clean.json which can then be used to
produce human readable diffs for code reviews of npm dependency updates.

Author: IgorMinar