Take a different approach to working around deduplication cleverness in click, this time hopefully without breaking hooks.

live-build/ubuntu-touch/hooks/60-install-click.chroot

@@ -16,15 +16,8 @@ chown clickpkg:clickpkg "$click_db"
 mkdir -p -m 755 "$click_db_custom"
 chown clickpkg:clickpkg "$click_db_custom"
 
-# move default configuration aside to stop click being clever about symlink
-# layering
-mv /etc/click/databases /etc/click/databases.tmp
-
 tmpdir="$(mktemp -d)"
-cleanup () {
-    rm -rf "$tmpdir"
-    mv /etc/click/databases.tmp /etc/click/databases
-}
+cleanup () { rm -rf "$tmpdir"; }
 trap cleanup EXIT
 
 CLICKARCH=$(dpkg --print-architecture)
@@ -55,8 +48,20 @@ do
                 ;;
         esac
         for root in $roots; do
+            if [ "$root" = "$click_db_custom" ]; then
+                # FIXME: there is no good way to stop click from
+                # deduplicating things when installing the same package in
+                # multiple databases; the best we can do is to temporarily
+                # pretend that the core database does not exist
+                mv /etc/click/databases/10_core.conf \
+                   /etc/click/databases/10_core.conf.tmp
+            fi
             click install --force-missing-framework --root="$root" --all-users \
                 "$tmpdir/$package"
+            if [ "$root" = "$click_db_custom" ]; then
+                mv /etc/click/databases/10_core.conf.tmp \
+                   /etc/click/databases/10_core.conf
+            fi
         done
     fi
 done