Configure created by autogen.sh doesn't add $prefix/include to include path?

[Darryl Rees <rees netnam vn>]

I am building gnome from cvs, parallel to standard RH8.0 gnome 2 which I 
use for everyday work. I download the bzip2 libraries as source and 
compile these into my parallel build as well, which creates a 
$PREFIX/include/bzip.h.
The configure script created for gnome-vfs by autogen.sh in gnome-common 
does not seem to look in $PREFIX/include, only in /usr/include. 
Therefore my configure script always fails and tells me I don't have the 
bzip libraries. If I copy or link bzip.h into /usr/include all goes well.
I believe the makefiles created are fine, they do look in $PREFIX. Put 
me straight, isn't this really bad? (I'm assuming this affects all gnome 
modules and not just gnome-vfs). Shouldn't the tests in configure use 
exactly the same include directories as the makefiles? I would have 
thought this could create all kinds of subtle build bugs on various 
configurations... or am I doing something completely stoopid.
Cheers
Darryl Rees.

PS. If the author of bzip happens to be reading, could please you please 
add an install target to the shared library makefile for bzip...