Uncaught exception Failure("input_value: bad bigarray kind")
This turns out to be caused by a change of serializer between ocaml 4.01 and 4.02. Unison compiled with 4.02 can't talk to pre-4.02 unisons successfully, and the reason mine failed this week is because I did some reinstalls following an upgrade to OS X Yosemite. So I had homebrew's unison compiled with 4.02+ and Ubuntu's unison on my server, compiled with 4.01.
Even if I updated the server to Ubuntu utopic unicorn, it wouldn't solve the problem. ocaml 4.02 didn't make it in because it wasn't released soon enough.
So, time to build unison from source against ocaml built from source!
One problem: ocaml 4.01 doesn't build against clang... and on Yosemite, that's all there is. I ended up hacking the ./configure script to delete all occurrences of the troublesome
-fno-defer-popflag, then redoing the install. Per the linked bug, it was added in the 01990s to avoid tickling a code generation bug in gcc-1.x. Newer clangs won't complain about this particular flag, and newer ocamls won't use it, but I chose to stick with the old (semi-current) versions of both.
Happily, that seemed to be the only problem, and the rest of the unison build (namely, the text UI; I didn't want a heap of dependencies) went fine.
(And this, friends, is why you should define a real file format, instead of just dumping your internal state out through your native serializer. For things you control, you can have much broader cross-compatibility.)