At this point, the two variants have to be supported, at least as installation targets of Debian packages.
Two initiatives are worth mentioning at this point:
* [a patch](https://lists.debian.org/20181202212535.GC11687@gaara.hadrons.org) has been proposed for dpkg-buildpackage to mark packages built on "merged `/usr`" hosts with a `Build-Tainted-By: merged-usr-via-symlinks`;
* the reproducible builds team has added a "merged `/usr`" variation to their setup, and have then [tagged](https://tests.reproducible-builds.org/debian/issues/unstable/paths_vary_due_to_usrmerge_issue.html) the Debian packages from unstable which had differences due to "merged `/usr`". It seems that ~61 packages were affected by differing builds; 32 from these have been fixed in unstable already.
At this point, the two variants have to be supported, at least as installation targets of Debian packages.
Two initiatives are worth mentioning at this point:
* [a patch](https://lists.debian.org/20181202212535.GC11687@gaara.hadrons.org) has been proposed for dpkg-buildpackage to mark packages built on "merged `/usr`" hosts with a `Build-Tainted-By: merged-usr-via-symlinks`;
* the reproducible builds team has added a "merged `/usr`" variation to their setup, and have then [tagged](https://tests.reproducible-builds.org/debian/issues/unstable/paths_vary_due_to_usrmerge_issue.html) the Debian packages from unstable which had differences due to "merged `/usr`". It seems that ~61 packages were affected by differing builds; 32 from these have been fixed in unstable already.