cfg-update improvements

Fixes #404 (closed)

Documentation probably needs to be updated.

This splits cfg-update into two commands, itself and module-update, which runs module updates (and is run automatically after merge, but cfg-update is not).

I've made some improvements to cfg-update too, as it will need it more since it doesn't run immediately after the module updates are run anymore. Duplicate updates are filtered, and the prompt is a little more verbose.