optimizer ignores baseUrl when run from different directory

[jwbay]

It seems r.js is overriding baseUrl with the directory it's run from when doing single-file optimization with main and out. I've got a stripped-down reproduction repo located here with notes.

Given a project like this:

/app
  |- main.js - application entry point
/configs
  |- build-config.js - r.js build configuration
  |- require-config.js - shared configuration between runtime and build
/libs
  |- jquery.js
/bin

Running the optimizer from a subdirectory like bin/ with r.js.cmd -o ../configs/build-config.js makes r.js try to resolve module locations relative to the working directory, bin/, instead of the provided baseUrl of ../, or the project root.

Any help is appreciated!