The variable CPPFLAGS, set in (any) makevars file (part of a linking set) contains a flag to add an include path that points into the directory where CLISP has been built (which may be totally unrelated to where CLISP is installed, or on another machine). This happens at least on NixOS (linux distribution) as well as NetBSD. Judging from how the makevars file is generated this probably affects all platforms, though.
On NixOS:
CPPFLAGS='-I/tmp/nix-build-clisp-2.49.drv-0/clisp-2.49/builddir/gllib'
On NetBSD:
CPPFLAGS='-I/usr/pkg/include -I/usr/include -I/work/lang/clisp/work/clisp-2.49/src/gllib'
This isn't causing any real harm, it's just a bit unesthetic.
these files are necessary to build the linkset.
they have to point to which clisp is building it and the data it uses.
since the bundled clisp modules keep their gnulib imports in the centralized place (same as clisp proper), this is necessary.