gistfile1.md

Here's the project structure:

project
  |--main/
      config.js
      app.js
  |--subproject/
      app.js

project/main is the baseUrl. The main app's config.js references "subproject" with:

paths: {
  "subproject" : "../subproject"
}

RequireJS is happy during development. I want the build to produce:

project
  |--main-built/
      app.js
  |--subproject-built/
      app.js

but currently the requirejs build adds "subproject" back into "main-built/" directory.

Right, normally would target project if doing a whole project optimization. However, if it is really that main and subproject are really two, fully separate projects, and you just want to share some config between them, then I would use the approach in the multiple out example, but in this case, for the var configs array of builds, you would be using modules instead of out, the first modules build would be for main, the second entry in configs would have a modules section just for subproject.