Clone the repository.
$ git clone git@github.com:okuryu/package-json-flatten.git
$ cd package-json-flatten
Make a branch your working.
$ git checkout -b your-branch
Testing is much easier.
$ npm install
$ npm test
Commit your changes with detailed message after passed tests.
$ git commit
Fork the package-json-flatten repository.
Push your changes into the forked repository.
$ git push origin your-branch
Finally you must be able to make a Pull Request on GitHub.
Also, GitHub official documents might be useful to you for more details.