diff --git a/usr.sbin/freebsd-update/freebsd-update.sh b/usr.sbin/freebsd-update/freebsd-update.sh
index ef63c0cfbe3..49db090aaa8 100644
--- a/usr.sbin/freebsd-update/freebsd-update.sh
+++ b/usr.sbin/freebsd-update/freebsd-update.sh
@@ -2814,15 +2814,23 @@ Kernel updates have been installed.  Please reboot and run
 
 	# If we haven't already dealt with the world, deal with it.
 	if ! [ -f $1/worlddone ]; then
+		# Create any necessary directories first
+		grep -vE '^/boot/' $1/INDEX-NEW |
+		    grep -E '^[^|]+\|d\|' > INDEX-NEW
+		install_from_index INDEX-NEW || return 1
+
 		# Install new shared libraries next
 		grep -vE '^/boot/' $1/INDEX-NEW |
+		    grep -vE '^[^|]+\|d\|' |
 		    grep -E '/lib/.*\.so\.[0-9]+\|' > INDEX-NEW
 		install_from_index INDEX-NEW || return 1
 
 		# Deal with everything else
 		grep -vE '^/boot/' $1/INDEX-OLD |
+		    grep -vE '^[^|]+\|d\|' |
 		    grep -vE '/lib/.*\.so\.[0-9]+\|' > INDEX-OLD
 		grep -vE '^/boot/' $1/INDEX-NEW |
+		    grep -vE '^[^|]+\|d\|' |
 		    grep -vE '/lib/.*\.so\.[0-9]+\|' > INDEX-NEW
 		install_from_index INDEX-NEW || return 1
 		install_delete INDEX-OLD INDEX-NEW || return 1
@@ -2868,11 +2876,20 @@ again to finish installing updates.
 
 	# Remove old shared libraries
 	grep -vE '^/boot/' $1/INDEX-NEW |
+	    grep -vE '^[^|]+\|d\|' |
 	    grep -E '/lib/.*\.so\.[0-9]+\|' > INDEX-NEW
 	grep -vE '^/boot/' $1/INDEX-OLD |
+	    grep -vE '^[^|]+\|d\|' |
 	    grep -E '/lib/.*\.so\.[0-9]+\|' > INDEX-OLD
 	install_delete INDEX-OLD INDEX-NEW || return 1
 
+	# Remove old directories
+	grep -vE '^/boot/' $1/INDEX-OLD |
+	    grep -E '^[^|]+\|d\|' > INDEX-OLD
+	grep -vE '^/boot/' $1/INDEX-OLD |
+	    grep -E '^[^|]+\|d\|' > INDEX-OLD
+	install_delete INDEX-OLD INDEX-NEW || return 1
+
 	# Remove temporary files
 	rm INDEX-OLD INDEX-NEW
 }