Optimize away most expensive file prune calls, when refreshing

Optimize away most expensive file prune calls, when refreshing

Benchmarking refresh of a a wiki with 25 thousand pages showed
file_pruned() using most of the time. But, when refreshing, ikiwiki already
knows about nearly all the files. So we can skip calling file_pruned() for
those it knows about. While tricky to do, this sped up a refresh (that
otherwise does no work) by 10-50%.