cli: "Unexpected token import" when using symlinks

I’m submitting a bug report

• Library Version: CLI: 0.32.0

Please tell us about your environment:

• Operating System: Windows 10 Pro

• Node Version: 9.5.0

• NPM Version: 5.6.0

• Browser: N/A

• Language: ESNext

• Loader/bundler: SystemJS and RequireJS

Current behavior: au new --here does it’s thing. After installing dependencies, I run au build, and get the error:

(function (exports, require, module, __filename, __dirname) { import gulp from 'gulp';
                                                              ^^^^^^

SyntaxError: Unexpected token import
    at new Script (vm.js:51:7)
    at createScript (vm.js:138:10)
    at Object.runInThisContext (vm.js:199:10)
    at Module._compile (module.js:624:28)
    at Module._extensions..js (module.js:671:10)
    at Object.require.extensions.(anonymous function) [as .js] (d:\code\scratch\meh\node_modules\babel-register\lib\node.js:152:7)
    at Module.load (module.js:573:32)
    at tryModuleLoad (module.js:513:12)
    at Function.Module._load (module.js:505:3)
    at Module.require (module.js:604:17)

I have just recently reformatted my machine, this is a fresh box with everything installed first time.

I have a .babelrc file (put there by the CLI):

{
  "sourceMap": true,
  "sourceRoot": "src",
  "moduleIds": false,
  "comments": false,
  "compact": false,
  "code": true,
  "presets": [
    ["es2015", {"loose": true}],
    "stage-1"
  ],
  "plugins": [
    "syntax-flow",
    "transform-decorators-legacy",
    "transform-flow-strip-types"
  ]
}

• What is the expected behavior? I’d like it to build!

• What is the motivation / use case for changing the behavior? 😐