diff --git a/Dockerfile-alpine.template b/Dockerfile-alpine.template
index db405303..289dfda2 100644
--- a/Dockerfile-alpine.template
+++ b/Dockerfile-alpine.template
@@ -111,8 +111,7 @@ RUN set -ex; \
     chmod +x /usr/src/nextcloud/occ; \
     apk del .fetch-deps
 
-COPY *.sh /
-COPY config/* /usr/src/nextcloud/config/
+COPY rootfs /
 
 ENTRYPOINT ["/entrypoint.sh"]
 CMD ["%%CMD%%"]
diff --git a/Dockerfile-debian.template b/Dockerfile-debian.template
index ab6f88f9..9cdebe8b 100644
--- a/Dockerfile-debian.template
+++ b/Dockerfile-debian.template
@@ -126,8 +126,7 @@ RUN set -ex; \
     apt-get purge -y --auto-remove -o APT::AutoRemove::RecommendsImportant=false $fetchDeps; \
     rm -rf /var/lib/apt/lists/*
 
-COPY *.sh /
-COPY config/* /usr/src/nextcloud/config/
+COPY rootfs /
 
 ENTRYPOINT ["/entrypoint.sh"]
 CMD ["%%CMD%%"]
diff --git a/update.sh b/update.sh
index 263935a7..75fa0c24 100755
--- a/update.sh
+++ b/update.sh
@@ -80,17 +80,22 @@ function create_variant() {
 		s/%%REDIS_VERSION%%/'"${pecl_versions[redis]}"'/g;
 	' "$dir/Dockerfile"
 
+	rootfs_dir="$dir/rootfs"
+	mkdir -p "$rootfs_dir"
+
 	# Copy the shell scripts
 	for name in entrypoint cron; do
-		cp "docker-$name.sh" "$dir/$name.sh"
+		cp "docker-$name.sh" "$rootfs_dir/$name.sh"
 	done
 
 	# Copy the config directory
-	cp -rT .config "$dir/config"
+	src_dir="$rootfs_dir/usr/src/nextcloud"
+	mkdir -p "$src_dir"
+	cp -rT .config "$src_dir/config"
 
 	# Remove Apache config if we're not an Apache variant.
 	if [ "$variant" != "apache" ]; then
-		rm "$dir/config/apache-pretty-urls.config.php"
+		rm "$src_dir/config/apache-pretty-urls.config.php"
 	fi
 
 	for arch in i386 amd64; do