I’ve got the Pd patches running from /usr/local/...-patches/[my_folder] via the app 
I copied the .yml from the basic patch in this tutorial:
name: Basic patch
author: Giedrius
entry: basic.pd
image: basic.jpeg
description: |
A demo patch for the controls.
tags:
- simple
- controls
- demo
and edited it with the details of my patch, then added that to /usr/local/...-patches/[my_folder] and copied the image file from the tutorial there too.
Opened the app, it showed up in collections, and it works fine