A clear is someone who is proven to be sided with the village, usually through an undeniable logical process.
Much like the word "prove" itself, the meaning of "clear" varies on context. In a game with investigations and a (cleared) cop, an inno report clears whoever the report is on. However, in a setup without investigations or with no further investigations possible (e.g. cop died), players may use the term loosely ("billking is cleared. He's way too pro-town to possibly be scum.").