Pydio is open source software, and the code is published under the AGPLv3 License. As such, the code is publicly available on GitHub, and forking is particularly recommended! Still, contribution must be done following some guidelines.
Please read before contributing
Pydio currently has two main products : Pydio 8 (PHP stack) and Pydio Cells (Golang).
Let's be franck, the latter has the favour of the core team and unless you find a simple bugfix or a security issue in Pydio 8, we strongly discourage you to contribute on Pydio 8. Our bandwith is not so big, and we will probably not take the time to inspect and merge any complex Pull-Request on this product. It will be maintained for vulnerability until end of 2019 (and one more year for Enteprise Distribution).
You should instead dig the code of Pydio Cells! Go is the future, and it's fun! The best starting point is the developer guide where we describe the architecture and basic concepts.
GH organization & Pull Requests
The code is located at https://github.com/pydio/cells. From here, you can fork to write your own services or provide bug fixes. The project is organized to use the master branch by default. Make sure to fork and submit PR on this branch only. Once you are happy with your code, please use the standard Github "Pull Request" mechanism to submit your changes. If you are not familiar with git, reading https://help.github.com/articles/using-pull-requests is a good start.