I clicked the "clean" button instead of "munge." What does a clean do?

And is it done

Clean deletes files from certain folders that are used to make the final lvl files you see in your addon folder, along with the compiled lvl files that are copied over to the addon folder, so the munge can start fresh instead of using old data. The main map assets always get cleaned when you do this, but you can select the rest as you may require. Mostly, you only really need to clean when new changes aren't showing up ingame, or you get those "bracket expected" errors in the mungelog because of a bad munge.

When it says "munge process finished", it's done.