Ask HN: Whats you're ideal PhD workflow

I'll be starting a CS PhD (specifically comp bio/biomedical datascience) at Columbia this September and have been thinking a lot about what sort of workflow/tech stack would be best to use during this period of time. I've only ever worked in academic research and haven't always had the most structure which would usually resemble a waterfall type workflow.

So far I'm thinking kanban to organize ToDos, SciWheel for citation management, Evernote for general notetaking, overleaf for LaTeX, and Doom Emacs as an IDE all used in an Agile-esque way.

Are there any suggested organizational methods/tools that you might recommend?