"Cleanup" clears inbox unintentionally
 

I like keeping tasks in my inbox, even when they have automatically set contexts (from Mail) or I gave them contexts (from quick entry), until I'm explicitly processing the Inbox. This is so I can make sure they go to the right place in a project and I can make sure they're actionable and so on.

I also like checked-off things disappearing as soon as I check them off. (Or I'd be happy if they sorted to the bottom, or otherwise got out of my face. Grey is nice but doesn't cut it.) In get this behaviour now, I have to click "Cleanup". The problem is this cleans my inbox when I don't want it to.

I don't want to have to process my inbox continuously during the day. I do that once in the evening. I don't want checked-off items cluttering up my todo list. Why can't cleanup be sensitive to the current view, and only clear things out of the inbox when I'm looking at it?