Hah. I was looking into one of the other packages you mentioned,
elixir-cmd, and at the bottom of its readme it has:
it is active when the project has a mix file in its root directory
At some point in the past, I started using Atom at the base directory of my repo and not the umbrella app. This has brought back the functions. I wonder if
atom-elixir works now.
Edit: Submitted a PR for the readme.