Remove clean as configuration option

[jayqi]

Setting clean=True in the configuration is dangerous, because it will delete things without user input and can lead to data loss.

It might be a good idea to add a prompt to the configure command where if a user sets clean=True, they need to read a warning and confirm that they want to configure things that way.

For now, we should just remove clean from the configuration and from the post-save hook. This isn't mature enough to let users run automatically.