IIUC, what you're trying to do is not recommended by the GNU
standards, this is why it's hard to performed.  The motivation is that
you should be able to

        make prefix=/foo

so `configure' is not supposed to hard code the value of `prefix' that
it knows.

At least for part of your issue, the problem might be solved thanks to
a macro from Alexandre Oliva :

http://research.cys.de/autoconf-archive/Miscellaneous/ac_define_dir.html

        Akim

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