NPM Package Directory Mess - json

Question

While ago when I run npm install under my project it installed all node modules correctly and nicely by installing all packages that I have defined under packages.json file.
Now that I have updated npm and node to latest version and when I run npm install 90% of sub directories of npm packages will be installed under node_modules folder. Thus it will look so messy. Here's the picture of the folders: (I couldn't get all the folders since resolution is limited)
and here's my package.json file:
{
"name": "my-application",
"description": "description here...",
"repository": {
"type": "git",
"url": ""
},
"version": "0.0.1",
"devDependencies": {
"grunt": "~0.4.1",
"grunt-autoprefixer": "~0.4.0",
"grunt-bower-install": "~0.7.0",
"grunt-concurrent": "~0.4.1",
"grunt-connect-proxy": "~0.2.0",
"grunt-connect-socket.io": "^0.7.1",
"grunt-contrib-clean": "~0.5.0",
"grunt-contrib-coffee": "~0.7.0",
"grunt-contrib-compass": "~1.0.1",
"grunt-contrib-concat": "~0.3.0",
"grunt-contrib-connect": "~0.11.2",
"grunt-contrib-copy": "~0.4.1",
"grunt-contrib-cssmin": "~0.7.0",
"grunt-contrib-htmlmin": "~0.1.3",
"grunt-contrib-imagemin": "~0.3.0",
"grunt-contrib-jshint": "~0.7.1",
"grunt-contrib-uglify": "~0.2.0",
"grunt-contrib-watch": "~0.5.2",
"grunt-fixmyjs": "0.2.0",
"grunt-google-cdn": "~0.2.0",
"grunt-karma": "~0.6.2",
"grunt-newer": "~0.5.4",
"grunt-ngmin": "~0.0.2",
"grunt-rev": "~0.1.0",
"grunt-usemin": "~2.0.0",
"jasmine": "~2.3.1",
"jshint-stylish": "~0.1.3",
"jshint-stylish-ex": "^0.2.0",
"karma": "~0.10.8",
"karma-chrome-launcher": "~0.1.1",
"karma-coffee-preprocessor": "~0.1.1",
"karma-firefox-launcher": "~0.1.2",
"karma-html2js-preprocessor": "~0.1.0",
"karma-jasmine": "~0.1.5",
"karma-ng-html2js-preprocessor": "~0.1.0",
"karma-ng-scenario": "~0.1.0",
"karma-phantomjs-launcher": "~0.1.1",
"karma-requirejs": "~0.2.0",
"karma-script-launcher": "~0.1.0",
"load-grunt-tasks": "~0.2.0",
"requirejs": "~2.1.9",
"socket.io": "~1.3.7",
"socket.io-client": "^1.3.7",
"time-grunt": "~0.2.1"
},
"engines": {
"node": ">=0.8.0"
},
"scripts": {
"test": "grunt test"
}
}
How I can tell to npm to install/arrange directories properly?
NPM version: 3.5.0
Node version: 5.1.0
I use grunt to run the project.

Answer 1

With npm 3 your dependencies will now be installed flat - by default. If possible, all of your dependencies, and their dependencies, and their dependencies will be installed in your project's node_modules folder without nesting. Nesting will only occur when two or more modules have conflicting dependencies.
This was done because in windows there's restriction on maximum path length.