> Also, since all sub package have basically their own 
> configure script (with many common parts), I feel it was 
> smarter to use one unique configure script...
> But maybe I were wrong...
> 
> How do you advice me to make a recursive compilation of sub package?

Just have a Makefile that descends into each sub directory, runs
configure in that directory (with appropriate enables/disables that you
need) then runs make in that directory.


> in particular when all are using autotools but fltk wich 
> seems to Cmake?

No, fltk uses autoconf. It also has some Cmake support, but that is not
the (current) primary configuration scheme. It *might* be the preferred
soultion in the future, but 1.1.9 (which is what you bundled) uses
autoconf.



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