Invalid configuration object. Webpack has been initialised using a configuration object that does not match the API schema

Just change from "loaders" to "rules" in "webpack.config.js"

Because loaders is used in Webpack 1, and rules in Webpack2. You can see there have differences.

I solved this issue by removing empty string from my resolve array. Check out resolve documentation on webpack's site.

//Doesn't work
module.exports = {
  resolve: {
    extensions: ['', '.js', '.jsx']
  }
  ...
}; 

//Works!
module.exports = {
  resolve: {
    extensions: ['.js', '.jsx']
  }
  ...
};

I don't exactly know what causes that, but I solve it this way.
Reinstall whole project but remember that webpack-dev-server must be globally installed.
I walk through some server errors like webpack cant be found, so I linked Webpack using link command.
In output Resolving some absolute path issues.

In devServer object: inline: false

webpack.config.js

module.exports = {
    entry: "./src/js/main.js",
    output: {
        path:__dirname+ '/dist/',
        filename: "bundle.js",
        publicPath: '/'
    },
    devServer: {
        inline: false,
        contentBase: "./dist",
    },
    module: {
        loaders: [
            {
                test: /\.jsx?$/,
                exclude:/(node_modules|bower_components)/,
                loader: 'babel-loader',
                query: {
                    presets: ['es2015', 'react']
                }
            }
        ]
    }

};

package.json

{
  "name": "react-flux-architecture-es6",
  "version": "1.0.0",
  "description": "egghead",
  "main": "index.js",
  "scripts": {
    "start": "webpack-dev-server"
  },
  "repository": {
    "type": "git",
    "url": "git+https://github.com/cichy/react-flux-architecture-es6.git"
  },
  "keywords": [
    "React",
    "flux"
  ],
  "author": "Jarosław Cichoń",
  "license": "ISC",
  "bugs": {
    "url": "https://github.com/cichy/react-flux-architecture-es6/issues"
  },
  "homepage": "https://github.com/cichy/react-flux-architecture-es6#readme",
  "dependencies": {
    "flux": "^3.1.2",
    "react": "^15.4.2",
    "react-dom": "^15.4.2",
    "react-router": "^3.0.2"
  },
  "devDependencies": {
    "babel-core": "^6.22.1",
    "babel-loader": "^6.2.10",
    "babel-preset-es2015": "^6.22.0",
    "babel-preset-react": "^6.22.0"
  }
}