Babel 5 (needed by ryuu) vs 6 breaks script runner

[hut8]

I'm running to an issue running npm run upload. I've done some debugging and here's what I found:

npm run upload runs npm run build && cd dist/ && domo publish && cd ..

The project builds fine, but then during domo upload I get:

[ERROR] The domo cli tool has experienced an error. As it is
[ERROR] possible this bug has already been fixed, please try updating
[ERROR] using `npm install -g ryuu` and run this command again. If this
[ERROR] does not fix the issue, please contact your MajorDomo.
[ERROR] error message: [BABEL] /home/liam/myprojectpath/node_modules/ryuu/bin/domo.js: Using removed Babel 5 option: base.stage - Check out the corresponding stage-x presets http://babeljs.io/docs/plugins/#presets

I noticed that this is originating in the node_modules folder, so it's not using the global installation of ryuu as documented at developer.domo.com. I tried running cd dist; domo publish in the shell (as opposed to the script runner) and it worked fine!

I see that in package.json, there's "babel-core": "^6.3.17" but that shouldn't matter since in node_modules/ryuu/package.json there's "babel": "5.8.12". I was very confused when I went into the node_modules of ryuu (i.e., starter-kit/node_modules/ryuu/node_modules/) and didn't find babel at all. So it's easy to see that for some reason ryuu starts using babel 6 from starter-kit. I'm not a Node expert, so this comes as a surprise to me.

I'm using npm 4.0.3 (I just reproduced it on 3 though, so I figured maybe there was some bug causing this and upgraded to 4) and node 7.1.0. I'm on Linux.