require('babel-register');
require('./src/app.js');

import package from 'package';
...

#!/usr/bin/env node
require('../bootstrap.js');

appdir$ ./bin/myapp
I'm running fine!
appdir$

$ sudo npm install -g myapp
└── myapp@0.1.0
$ myapp
/usr/local/lib/node_modules/myapp/src/app.js:1
(function (exports, require, module, __filename, __dirname) { import package from 'package';
                                                              ^^^^^^

SyntaxError: Unexpected token import
    at exports.runInThisContext (vm.js:53:16)
    at Module._compile (module.js:404:25)
    at Module._extensions..js (module.js:432:10)
    at Object.require.extensions.(anonymous function) [as .js] (/usr/local/lib/node_modules/myapp/node_modules/babel-register/lib/node.js:138:7)
    at Module.load (module.js:356:32)
    at Function.Module._load (module.js:313:12)
    at Module.require (module.js:366:17)
    at require (module.js:385:17)
    at Object.<anonymous> (/usr/local/lib/node_modules/myapp/server.js:9:12)
    at Module._compile (module.js:425:26)

├─┬ babel-register@6.4.3
    │ │ ├─┬ babel-core@6.4.5
    │ │ │ ├─┬ babel-code-frame@6.3.13
    │ │ │ ├─┬ babel-generator@6.4.5
    │ │ │ ├── babel-helpers@6.4.5
    │ │ ├── babel-runtime@5.8.35

require('babel-register')({
  ignore: false,
  only: /myapp/src/
});
require('./src/app.js');

$ sudo npm install -g node-inspector

$ node-debug --debug-brk myapp

babel-register/lib/node.js:120:
function shouldIgnore(filename) {
  if (!ignore && !only) {  // here `ignore` and `only` were null, despite .babelrc values
    return getRelativePath(filename).split(_path2["default"].sep).indexOf("node_modules") >= 0;
  } else {
    return _babelCore.util.shouldIgnore(filename, ignore || [], only);
  }
}