Since April 2021, several gnulib-tool invocations are supported in the scope of the same configure.ac.
But there's a limitation to that: It does not really work well with compilers that don't support #include_next (such as MSVC). Namely, let's look what happens if there are two gnulib-tool invocations gnulib-tool --source-base=dir1 ... gnulib-tool --source-base=dir2 ... Assume that in dir1, there is an override of function A in <stdlib.h>, and that in dir2, there is an override of function B in <stdlib.h>. Code that uses both dir1 and dir2 will be compiled with options -Idir1 -Idir2 or -Idir2 -Idir1 On platforms which support #include_next, the files dir1/stdlib.h and dir2/stdlib.h will enhance each other, that is, both overrides of A and B will become active. Whereas on platforms without #include_next: * Options '-Idir1 -Idir2' activate dir1/stdlib.h, and dir2/stdlib.h is ignored. * Options '-Idir2 -Idir1' activate dir2/stdlib.h, and dir1/stdlib.h is ignored. Fortunately this limitation is not encountered frequently. But nevertheless, we need to remember that two different generated stdlib.h files can lead to trouble, and likewise for any other Gnulib-generated .h file. I don't see an easy fix. Bruno