Node Red deployable file

Yes, that's the default. Easy for beginners. This initial complexity is why the default is as it is.

You simply need to adjust your startup. Here, for example is the package.json in my master Node-RED folder:

{
  "name": "node-red-master",
  "version": "0.19.0",
  "description": "Test environment for developing Node-RED flows",
  "main": "index.js",
  "scripts": {
    "start": "node node_modules/node-red/red.js --userDir ./data",
    "update": "npm install --unsafe-perm node-red",
    "check": "npm outdated",
    "check-data": "cd data && npm outdated",
    "update-data": "cd data && npm update",
    "check-master": "npm outdated",
    "update-master": "npm update",
    "log": "sudo journalctl -u nrlive -f -n 0 -o cat"
  },
  "keywords": [
    "node-red"
  ],
  "author": "Julian Knight",
  "license": "MIT",
  "dependencies": {
    "node-red": "^0.19.4"
  }
}

With that, you can start Node-RED manually simply by typing npm start on the command line when in that folder. Note that Node-RED itself is the only package installed in that folder.

Also note that my userDir folder is called data and it sits inside that master folder.