After upgrading to Visual Studio 2015, Multi-Device Hybrid Apps (Cordova based apps) have a new project structure and are incompatible with VS. Microsoft have released a how-to guide here for upgrading your projects but due to it not being visible on search engines, being a little bit lacking in depth and taking me about half an hour to find the instructions - I have decided to replicate it here (with some extra details missing from the original). So, in order to update your previous project to the new structure, follow these steps;

  1. Make a backup of your existing project
  2. Create a new project using the JavaScript > Apache Cordova Apps > Blank App template
    • For TypeScript projects, you can use the TypeScript equivalent of this same project
  3. Copy the .jsproj and taco.json files created by this template into your own project's folder
  4. In your project, create a new folder named www
  5. Delete the following folders from your project's folder:
    • bin
    • bld
  6. Leave the following folders/files in your project directory:
    • merges
    • res
    • plugins
    • config.xml
  7. Copy all other files/folders into the www folder
  8. In the res folder, if you have a cert directory, rename it to native
  9. If you're using TypeScript, you'll need to add a tsconfig.json to your project folder and define config settings for your project – see more in the Configuring TypeScript section on the original Microsoft article linked above
  10. Now you can build and run your application

If you have errors, you may need to update file references to reflect the new folder structure.

Lastly, you should add the following XML elements to your config.xml (inside the <widget> element) to ensure your icons and splash screens are picked up by right clicking on the file and selecting "View Code":

 
<platform name="android">
<icon src="res/icons/android/icon-36-ldpi.png" density="ldpi" />
<icon src="res/icons/android/icon-48-mdpi.png" density="mdpi" />
<icon src="res/icons/android/icon-72-hdpi.png" density="hdpi" />
<icon src="res/icons/android/icon-96-xhdpi.png" density="xhdpi" />
</platform>

<platform name="ios">
<icon src="res/icons/ios/icon-60-3x.png" width="180" height="180" />
<icon src="res/icons/ios/icon-60.png" width="60" height="60" />
<icon src="res/icons/ios/icon-60-2x.png" width="120" height="120" />
<icon src="res/icons/ios/icon-76.png" width="76" height="76" />
<icon src="res/icons/ios/icon-76-2x.png" width="152" height="152" />
<icon src="res/icons/ios/icon-40.png" width="40" height="40" />
<icon src="res/icons/ios/icon-40-2x.png" width="80" height="80" />
<icon src="res/icons/ios/icon-57.png" width="57" height="57" />
<icon src="res/icons/ios/icon-57-2x.png" width="114" height="114" />
<icon src="res/icons/ios/icon-72.png" width="72" height="72" />
<icon src="res/icons/ios/icon-72-2x.png" width="144" height="144" />
<icon src="res/icons/ios/icon-small.png" width="29" height="29" />
<icon src="res/icons/ios/icon-small-2x.png" width="58" height="58" />
<icon src="res/icons/ios/icon-50.png" width="50" height="50" />
<icon src="res/icons/ios/icon-50-2x.png" width="100" height="100" />
</platform>

<platform name="windows">
<icon src="res/icons/windows/Square150x150Logo.scale-100.png" width="150" height="150" />
<icon src="res/icons/windows/Square150x150Logo.scale-240.png" width="360" height="360" />
<icon src="res/icons/windows/Square30x30Logo.scale-100.png" width="30" height="30" />
<icon src="res/icons/windows/Square310x310Logo.scale-100.png" width="310" height="310" />
<icon src="res/icons/windows/Square44x44Logo.scale-240.png" width="106" height="106" />
<icon src="res/icons/windows/Square70x70Logo.scale-100.png" width="70" height="70" />
<icon src="res/icons/windows/Square71x71Logo.scale-240.png" width="170" height="170" />
<icon src="res/icons/windows/StoreLogo.scale-100.png" width="50" height="50" />
<icon src="res/icons/windows/StoreLogo.scale-240.png" width="120" height="120" />
<icon src="res/icons/windows/Wide310x150Logo.scale-100.png" width="310" height="150" />
<icon src="res/icons/windows/Wide310x150Logo.scale-240.png" width="744" height="360" />
</platform>

<platform name="wp8">
<icon src="res/icons/wp8/ApplicationIcon.png" width="62" height="62" />
<icon src="res/icons/wp8/Background.png" width="173" height="173" />
</platform>

<platform name="android">
<splash src="res/screens/android/screen-hdpi-landscape.png" density="land-hdpi"/>
<splash src="res/screens/android/screen-ldpi-landscape.png" density="land-ldpi"/>
<splash src="res/screens/android/screen-mdpi-landscape.png" density="land-mdpi"/>
<splash src="res/screens/android/screen-xhdpi-landscape.png" density="land-xhdpi"/>
<splash src="res/screens/android/screen-hdpi-portrait.png" density="port-hdpi"/>
<splash src="res/screens/android/screen-ldpi-portrait.png" density="port-ldpi"/>
<splash src="res/screens/android/screen-mdpi-portrait.png" density="port-mdpi"/>
<splash src="res/screens/android/screen-xhdpi-portrait.png" density="port-xhdpi"/>
</platform>

<platform name="ios">
<splash src="res/screens/ios/screen-iphone-portrait.png" width="320" height="480"/>
<splash src="res/screens/ios/screen-iphone-portrait-2x.png" width="640" height="960"/>
<splash src="res/screens/ios/screen-ipad-portrait.png" width="768" height="1024"/>
<splash src="res/screens/ios/screen-ipad-portrait-2x.png" width="1536" height="2048"/>
<splash src="res/screens/ios/screen-ipad-landscape.png" width="1024" height="768"/>
<splash src="res/screens/ios/screen-ipad-landscape-2x.png" width="2048" height="1536"/>
<splash src="res/screens/ios/screen-iphone-568h-2x.png" width="640" height="1136"/>
<splash src="res/screens/ios/screen-iphone-portrait-667h.png" width="750" height="1334"/>
<splash src="res/screens/ios/screen-iphone-portrait-736h.png" width="1242" height="2208"/>
<splash src="res/screens/ios/screen-iphone-landscape-736h.png" width="2208" height="1242"/>
</platform>

<platform name="windows">
<splash src="res/screens/windows/SplashScreen.scale-100.png" width="620" height="300"/>
<splash src="res/screens/windows/SplashScreen.scale-240.png" width="1152" height="1920"/>
<splash src="res/screens/windows/SplashScreenPhone.scale-240.png" width="1152" height="1920"/>
</platform>

<platform name="wp8">
<splash src="res/screens/wp8/SplashScreenImage.jpg" width="480" height="800"/>
</platform>