Contextualise. Contextualise is an effective tool particularly suited for organising information-heavy projects and activities consisting of unstructured and widely diverse data and information resources.
I'm finishing a mathematical art project I started in 2007 and then left sitting for about seventeen years. It's technically not open-source yet, since only I have the code, but the code will be fully published under an open license with the results.
GitHub: https://github.com/brettkromkamp/contextualise
Website: https://contextualise.dev/