npm install into a subfolder of your choice!

README.md

In your package.json file add the following two script declarations:

"scripts": {
    "preinstall": "node preinstall.js",
    "postinstall": "node postinstall.js"
},

In your entry script, add the followig code to make sure the working directory is set to the script so the node_modules folder resolves correctly:

process.chdir(__dirname);

postinstall.js

var fs = require("fs");
try
{
	if(process.platform.indexOf("win32") !== -1)
	{
		fs.unlinkSync("./node_modules/");
	}
	else
	{
		fs.unlinkSync("./node_modules");
	}
}
catch(e){}

preinstall.js

var fs = require("fs");
try
{
	fs.mkdirSync("./app/node_modules/");
}
catch(e)
{
}

try
{
	if(process.platform.indexOf("win32") !== -1)
	{
		fs.symlinkSync("./app/node_modules/","./node_modules/","junction");
	}
	else
	{
		fs.symlinkSync("./app/node_modules/","./node_modules","dir");
	}
}
catch(e){}