The change from /System/Links to /System/Index was done in part because of the issues with packaging. While Links used a gobo unique set of directory names to

The change from /System/Links to /System/Index was done in part because of the issues with packaging. While Links used a gobo unique set of directory names to house the symlinks, Index basically acts like /usr/local. meaning that these days a compile is done pretty much as if one would do ./configure --prefix=/usr/local. But the install stage is captured by a union mount and the files transferred to their designated location in /Programs. Sadly this change makes it that much harder to run Gobolinux in Rootless form out of a home dir or similar.