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These files are used to add OS, distribution and/or release specific
parameters, tests, etc. to ./configure

Brief instructions

begin with 

#!/bin/sh

echo "        Setting XXXXXX specific flag values"

All non error/warning echo's should be indented 8 spaces for neatness...

Common things to set are

LDFLAGS="${LDFLAGS} -L/usr/X11R6/lib"
CPPFLAGS="${CPPFLAGS} -lz -lm"

(note that you should always use those formats so that any other settings are
preserved).  The ${} can be first (takes effect first) or last.

You can also use other shell commands, such as testing if a file exists:

if ! test -f /usr/X11R6/lib/libXpm.so; then

You can use case statements on the preset values target and CC to do more detailed
version specific settings (note target is set by config.guess):

case "${CC}" in
    gcc* )
        ...stuff...
    ;;
esac

Finally, if you output a warning, set the flag value:

HAS_WARNING="yes"

You can do pretty much anything you can do in configure.
But you can not do all the things you can do in configure.in - you 
can NOT use autoconf macros in here.  If you really want to, look
at functions - there's a stripped down 'AC_CHECK_HEADER' function
(look at HPUX to see how to invoke it).