How to structure a JavaScript project?

You shouldn't specify the routing info on your js file names, those are the namespace and folder paths' jobs. So stackoverflow/util/HashMap.js is just fine. And you can use define("stackoverflow/util/HashMap", ....) to tell the dependency.

If you need to put your modules in a different folders, you can config paths for your loader, see this manual from RequireJS API.

There's no best way for structure your js files. But put the root namespace in a src folder is always a good practice. You can see the dojo source code and YUI source code and use similar ways for your project. They both are large scale Javascript projects.

actually it's better to get js lib routing to load all js using standard interface: "js.yoursite.com/lib-0.2.js" there should be a router (php or other, and able to cache queries). So there you could determine and control whole pathes that you use. Because common jquery plugin should stay at one dir, with jquery, and your own custom plugins not.

And there you control each project by it's own rules:

jquery/
  plugins/
    jquery.prettyPhoto.js
  jquery.min.js

mySuperJS/
  stable.0/ -- there your production version for 1.0 branch
    module.js
  0.1/
    module.js
  0.2/
    module.js
  0.3/
    module.js

myOtherlib/
  stable.0/ -- production version for all 0.* versions
  stable.1/ -- production version for all 1.0 versions
  0.1/
  0.2/
  0.3/
  0.4/
  0.4.1/
  0.4.1.18/

We're using such structure around a year and it's the best for us. But sometimes we use more complex solution and separate all modules for libs, plugins, tools, components and apps.