extension.json

{
  "ResourceModules": {
    "joaquin.js": {
       "scripts": "joaquin.js"
    },
    "jon.js": {
       "scripts": "jon.js"
    },
    "baha.js": {
       "scripts": "baha.js"
    },
    "others/sam.js": {
       "scripts": "others/sam.js"
    }
    "others/jeff.js": {
       "scripts": "others/jeff.js"
    }
  }
}

jeff.js

// (imagine this is inside a folder called other - gist wont let me do that)
var baha = require( 'baha.js' );

module.exports = {
  understand: function () {
    return true;
  },
  bahaUnderstands: function () {
    return baha.understand();
  },
  wtf: function () {
    return false;
  }
};

joaquin.js

var jon = require( 'jon.js' );
var jeff = require( 'others/jeff.js' );
var sam = require( 'others/sam.js' );

console.log( 'Is this thing on?', jon.understand() && sam.understand() && jeff.understand() && jeff.bahaUnderstands() );

jon.js

module.exports = {
  understand: function () {
    return true;
  },
  wtf: function () {
    return false;
  }
};

sam.js

// (imagine this is inside a folder called other - gist wont let me do that)
module.exports = {
  understand: function () {
    return true;
  },
  wtf: function () {
    return false;
  }
};