Fix hot code push client-side reloads.

We were overwriting the server directory when a client-side file changed,
which made all process calls fail, such as process.cwd() and fs.*. We
abstracted out some of the builder code so that only the client targets
are "rebuilt" when a client side file changes.
Add documentation
Merge branch 'packaging-fix-server-dir' into cordova-hcp

Conflicts:
	tools/bundler.js
Adjust tests for plugins
Fix cordova plugins test
Change saved path for cordova files