Thus far I've been solving some of these issues by symlinking to a folder "elm-stuff/local-packages". Then I add that package's src directory to elm-package.json. I like the way npm handles this with "npm link". Perhaps we could do something similar with "elm-package"? Let's say you have a fork of elm-core stored in ~/code/elm and want to use it in your app. Perhaps you could run:
elm-package link ~/code/elm/src
This command would then read that package's name from its elm-package.json, create a symlink under elm-stuff/packages/elm-core to ~/code/elm.
Just a thought, obviously there are many ways to solve this one.