After 695052e, the directories compat, dtrace, engines, flua, i18n and libxo now get created under /usr. This is one level higher than they should be.

The fix appears to be something like ..

diff --git a/etc/mtree/BSD.usr.dist b/etc/mtree/BSD.usr.dist
index 9f934976b77..95a711a4418 100644
--- a/etc/mtree/BSD.usr.dist
+++ b/etc/mtree/BSD.usr.dist
@@ -59,7 +59,6 @@
                     ..
                 ..
                 share
-                    ..
                 ..
             ..
         ..


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