Recently on startup I started getting an OpenSSH dialog warning me of an unknown host key. I then allowed it to store the key, and now I get a a password window at startup.
So then I went and cleared every known cache I could find, including recentf, .ido.last, and everything in my .emacs.d/savefile directory and it keeps bringing up of that OpenSSH password pop-up. What's even weirder is that the host it originally complained about not knowing the key for doesn't exist in my .ssh/known_hosts file, nor is there a system wide /etc/ssh/known_hosts file.
I can solve the problem of the pop-up from coming up every time by following the instructions here but I'm still quite miffed that I can't find the source of what file tramp is trying stat. It seems as if there is some other file I don't know about that's 1) caching some file on that host, and 2) some other unusual place that's caching the host's key.
Some other details: I'm running a prelude based emacs installation. Recently updated from Ubuntu 15.10 to 16.04 and wondering if that has anything to do with it.
~/.emacs.d/tramp, and restart. Tramp will write its current cached data to that file when Emacs shuts down, so deleting it while Emacs is still running won't help you. (You can undoubtedly clobber the necessary values within Emacs, but I don't know what they'd be offhand.) I don't know if this will solve your problem, but I think this is all the data Tramp caches between sessions.tramp-persistency-file-name, more correctly. For details, see thetramp-cachelibrary and its commentary.