Not only anticipate, but also guard against. For example, someone asked about a debugger. A specific debugger is simple: patch the debugger's source at compile time to hide the presence of the malware. Of course, that means you have to handle the case where the debugger is used to debug itself, too. That may pose a challenge, but given the existence of quines, I think it is possible. Doing that not for just _a_ debugger but every debugger in the world is left as an exercise.

Next, someone will look at timing and notice something strange. So, add stuff that tweaks the real-time clock to correct for this when your binary runs, when the OS gets built with your compiler. That way, running 'time' on your binary will not show anything suspicious.

Next, someone may notice a discrepancy between real-time clocks and their OS. Solution? Make sure analog clocks aren't that precise, hook all digital clocks up to a time signal, and tweak that signal if you hit slower code paths that the user shouldn't see. Also, make sure that all other computers in the world slow down whenever one of them hits one of these paths.

Next, someone will notice a discrepancy between clock time and solar time.

For that, the NSA made up the leap second.