PaperResources 
Let the minecraft client handle merging your resource packs natively. This paper plugin takes advantage of new features to tell players that join to load in multiple server resource packs!
Setup 
When the plugin loads up for the first time your can specify resource pack zip links on each line in /plugins/PaperResources/resources.txt and simply run /paperresources reload for your changes to take affect! This plugin works best if resource-pack in server.properties is left empty.
Developer API 
v2+ Includes access to the PaperResources API under the PaperResourcesManager class. JavaDocs are included with every release.
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