Error due to location of package.json file

I have an application whose structure is as follows:

• root:

  • main

    • node_modules

    • public folder

      • file1.js

      • file2.js

      • main.css

    • server.js

  • source folder

    • data.json
  • package.json

My application is working if I put the package.json file in the main folder and run "npm start" there. But if I try to run the program with the above structure, I am getting errors in accessing the file in the public folder and in the source folder. (no such directory or file found). My package.json file is as follows.

{
  "name": "arkadium",
  "version": "1.0.0",
  "description": "",
  "main": "main/server.js",
  "dependencies": {
    "body-parser": "^1.17.1",
    "cookie-parser": "^1.4.3",
    "ejs": "^2.5.5",
    "ejs-mate": "^2.3.0",
    "express-flash": "^0.0.2",
    "express": "^4.14.0",
    "express-session": "^1.15.2",
    "flash": "^1.1.0",
    "fs": "^0.0.1-security",
    "nodemon": "^1.11.0",
    "request": "^2.81.0",
    "xmlhttprequest": "^1.8.0"
  },
  "devDependencies": {},
  "scripts": {
    "start": "node main/server.js"
  },
  "author": "Arjun Dass",
  "license": "ISC"
}

Why am I getting this error when I am moving the package.json into the root directory? Even if I move the node_modules folder in the root directory, I am getting the same error. How can I get rid of this error. PS: I've been asked to maintain this structure.

via Arjun Dass