Oops, meant Notepad. They’re written in markdown and allow you to @ files. Turn it on in beta features then it should be below the timeline section

Be sure to add “do not unnecessarily delete code unless it does not align with our implementation or documentation” at the end of the previous prompt if it does this

Use the notebooks feature in beta instead of trying to force everything into .cursorrules. I’ve noticed they allow for better organization and help keep the agent on topic when trying to determine what changes need to be made.

Have you tried Nautilus? Sounds like an ideal use case if the research is academic.
nationalresearchplatform.org/nautilus/