AC_TRY_CPP/AC_CHECK_HEADER and --prefix != /usr/local

[Duncan Gibson]

Is there any reason why the includedir related to a user-supplied --prefix
(i.e. not /usr/local) isn't automatically added to the CPPFLAGS or internal
search path when looking for header files?

I installed fltk-1.1.0 with --prefix=/scratch/duncan

I'm trying to create a configure.in for my own application, also to be 
installed under /scratch/duncan. However if I use

        AC_TRY_CPP([#include <FL/Fl.H>],...)
or      AC_CHECK_HEADER([FL/Fl.H],...)
or      AC_CHECK_HEADERS([FL/Fl.H],...)

the configuration step fails, even if I set --prefix=/scratch/duncan

So far the only way round this is to set CPPFLAGS explicitly before
checking for the header file.

Is there a cleaner way?

Cheers
Duncan