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My friend and I are working on an application that already works for Windows 8 and is written in Javascript, HTML, and CSS. Our desire is to make it cross platform for areas like windows mobile, chrome, firefox, and android.

So, our directory structure looks like this:

.
├SomeApp.sln         // Visual Studio solution file
├SomeApp.suo         // other Visual Studio related file
├SomeApp.v11.suo     // other Visual Studio related file
├deploy.py           // Deployment script for apache
├Makefile            // For things like building the desktop version
│                    // and for testing/linting/deploying
conf
├── apache.conf
SomeApp
├── AppPackages
├── bin
│   ├── Debug
│   └── Release
├── bld
│   ├── Debug
│   └── Release
├── css
├── images
├── js
│   └── lib
├── pages
├── promo images
└── strings         // i18n language files
    ├── ar
    ├── bg
    ├── cs
    ├── da
    ├── de
    ├── el
    ├── en-US
    ├── es
    ├── fr
    ├── he
    ├── hr
    ├── hu
    ├── it
    ├── ja
    ├── ko
    ├── nb
    ├── nl
    ├── pl
    ├── pt
    ├── ro
    ├── ru
    ├── sv
    ├── tr
    ├── uk

I added things like the deploy script and the make file... but I'm really at a loss on how to organize a project like this. Would I create directories like this?

.
├──browserExtension/   
│  ├── build/           // put makefile here?           
│  ├── conf/            // put apache conf here?           
│  ├── chrome/      
│  ├── firefox/
├──web/                  // normal web page 
├──windows/                
│  ├── WindowsMobile8/      
│  └── Windows8/        // put existing solution files here?
├──mobile/       
│  ├── android/
└──common/
   ├── css/
   ├── js/
   │   └── test/
   └── html/

Is there a good example of a project that's already been successful doing this that I can follow?

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Just so you know, those ".suo" files are Visual Studio user options files. It stores information like which project is set as the startup project. You probably don't want to keep those in source control, since they're automatically generated and change frequently. –  Velociraptors May 20 '13 at 2:16

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