diff --git a/Makefile b/Makefile
index 4aac37a20..70506e6da 100644
--- a/Makefile
+++ b/Makefile
@@ -15,9 +15,13 @@ install: dependencies stack copyfiles plugins version
 
 copyfiles:
 	cp dokku /usr/local/bin/dokku
-	rm -Rf /var/lib/dokku/plugins
 	mkdir -p /var/lib/dokku/plugins
-	cp -r plugins/* /var/lib/dokku/plugins
+	find /var/lib/dokku/plugins -mindepth 2 -maxdepth 2 -name '.core' -printf '%h\0' | xargs -0 rm -Rf
+	find plugins/ -mindepth 1 -maxdepth 1 -type d -printf '%f\n' | while read plugin; do \
+	    rm -Rf /var/lib/dokku/plugins/$$plugin && \
+	    cp -R plugins/$$plugin /var/lib/dokku/plugins && \
+	    touch /var/lib/dokku/plugins/$$plugin/.core; \
+	    done
 
 version:
 	git describe --tags > ${DOKKU_ROOT}/VERSION  2> /dev/null || echo '~${DOKKU_VERSION} ($(shell date -uIminutes))' > ${DOKKU_ROOT}/VERSION