When I do a full build --- without clobbering --- where nothing related to js-ctypes has changed, the source files for libffi are recompiled and libffi is relinked. This is unnecessary and wasteful.

I see this too. It happens only when we rerun libffi's configure. Presumably that's invalidating too much and causes a full rebuild, and we want to bring it more in line with how ours work. What I don't know is whether our configure scripts a) generate a new Makefile every time configure is run, but our dependencies are such that a new Makefile alone won't cause a rebuild, or b) we detect that the output of configure is the same as the cached output and we don't regenerate Makefiles. Pretty sure it's b), but perhaps ted can confirm?

I don't think our configure tries to not remake makefiles every time. It is careful about a few other things, like mozilla-config.h: http://mxr.mozilla.org/mozilla-central/source/configure.in#8197 and autoconf.mk: http://mxr.mozilla.org/mozilla-central/source/configure.in#8354

Turns out all we need here is for libffi to have its own config.cache. This will be fixed by one of the patches in bug 538216.

Fixed per bug 538216.