Site has half-nuked itself

For reasons as yet unknown the site has utterly lost its mind.

It is being rebuilt or repaired as soon as I can figure out just what in all Hells is going on.

Most links should work, but many files/images seem to be under the impression they don’t exist.

This is definitely not a host issue — the files are all there unharmed.  This is not, I believe, a server configuration issue as everything attempts to resolve as expected.  I’m just starting to think I should very seriously shop around for WordPress alternatives as, clearly, this thing is not half so well written as it once was (other issues, luckily most of them invisible to readers, have been cropping up randomly now for several months).