bootstrap.js

const path = require('path');
const glob = require('glob');
const express = require('express');
const Bottle = require('bottlejs');

const bottle = Bottle.pop('MyPdfApp'); // name your instance here.

glob.sync(path.join(path.resolve(__dirname), 'app/**/*.js')).forEach((match) => {
  require(match); // just require, no need to pass the bottle reference.
});

// everything below is unchanged from your example

// App provider factory
const createApp = function(PdfController) {
  const app = express();
  app.post('/pdfs/:content_id', PdfController.create);
  
  return app;
}

bottle.service('app', createApp, 'controller.Pdfs');

// grab the application out of the container and start a server
const server = bottle.container.app.listen(3000, function () {
  var host = server.address().address;
  var port = server.address().port;

  console.log('Listening at http://%s:%s', host, port);
});

pdf-controller-factory.js

// Factory
function createPdfsController(container) {
  // the dependencies required by the service.  This is still lazily evaluated,
  // and mockable as long as you register the mock before accessing the service
  // in your tests.
  const PdfService = container.service.PdfGenerator;
  return {
    create: (req, res, next) => {
      const content_id = req.params.content_id;
      const pdf_id = PdfService.generate(content_id);
      res.json({ pdf_id: pdf_id });
    }
  };
}

// Export a function that registers the service provider with the given container.
modules.export = () => {
  require('bottlejs').pop('MyPdfApp').factory( // get the named container.
    'controller.Pdfs',   // the name of the service we're providing
    createPdfsController // the factory to create the service instance
  );
};