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If you have installed the devel package after having configured STklos, you'll have to run configure again. Normally, you should see the output of pkg-config in the file extensions/gtklos/lib/stklos/Makefile (to initialize the variable GTKFLAGS near line 345).
After applying the trick:
export STKLOS_GTK_DIR=/usr/lib/x86_64-linux-gnu
I got:
I have tried to edit it a bit, to fix the path:
#include <gtk-3.0/gtk/gtk.h>
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