Organise refactoring tasks

[dalonsoa]

This issue is mostly about creating new issues related to the refactoring of the existing code such that it follows best coding practices, including adopting design patterns and writing tests. The goal is to have a collection of issues that the research team can start working on under the supervision and review of the RSE Team.

The RSE Team will tackle some of the issues, but it will be mostly about coordinating efforts and reviweing PRs, and might extend beyond the official end of the project until funding is fully spent.