Sorry to followup on my own post, but I figured out what was going on. It
appears to be a problem with csup.
I've been using csup to maintain 2 CVS Repositories, one at home and one at
work.
The last couple of times I've run csup there were lots of 'checksum
mismatches',
so csup said it would download the entire file. I was watching it this morning
and saw it going through {/usr/src}/sys, usr.bin, and usr.sbin. It didn't,
however, actually download all of the files. When it said it was finished
(successfully!), the last file downloaded was in sys/netinet. This was on my
home system (amd64).
I tried on a machine a machine at work (i386) with the same results, except that
csup stopped downloading files much earlier. I restarted the csup; it picked up
where it left off (somewhere in sys/dev) complaining about checksum mismatches.
It then downloaded a fair number of files but still stopped before reaching
usr.bin. (Sorry I don't have hard numbers on how many files).
I installed cvsup. It picked up where csup had left off (also complaining about
checksums), but it updated everything and I've been able to buildworld and
buildkernel without any problems.
So my earlier problem was due to /usr/src/gnu being updated while
/usr/src/sys/sys wasn't :-( .
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