It looks like, because Make.common.in gets turned into Make.common at configure time, we can't currently configure with one prefix (or accidentally leave it defaulting to /usr/local) and install to another prefix and expect the result to be usable by applications that import our Make.common. I'm not sure how we'd fix this.
Oh wow, I didn't realize that was possible.
The fix may be to use a post-install hook to fix Make.common - I'll think about that...
Replace prefix at install time for 'make install prefix=/new/path' (#27)
I have addressed this with 8057190
make install prefix=/other/path
make installcheck prefix=/other/path
works just fine - the more pathological case of
make install prefix=/other/path exec_prefix=/yet/another/path
might take some more doing...
This works and has been added to my buildbot regimen.
Looks like the new netcdf broke this - I'll figure it out...