I might be wrong here as I am not very confident with neither guix nor guile.
I have guile installed in my home configuration, not in my system configuration (/etc/config.scm). Still, "/run/current-system/profile/share/guile/site/3.0" is in GUILE_LOAD_PATH environment variable. This is set by /etc/profile that sources "/run/current-system/profile/etc/profile". Moreover, "~/.guix-home/profile/share/guile/3.0 is not is GUILE_LOAD_PATH". Why?
