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Fix merge-usr.sh

Administrator requested to merge caleb/relative-usrmerge into master

Recent changes made the /usr merge symlinks inside the chroot absolute, so when inspected from outside they point into the hosts /usr/. This breaks a bunch of things in pmbootstrap (e.g. reading the apk db from /lib) and is generally dangerous.

Fix it and add a test. Additionally fix some issues this introduced in other tests.

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