I'm a grad student in Geomatics engineering, and I organize my workflow with a notebook and trello.
Notebook / Notepad: I've started transitioning away from notepads because loose sheets of paper aren't very good for long-term documentation. They are good for meetings and mocking something up, however, so I keep my notepad around for that, while I use a line-grid moleskine to document procedures / math that I am currently working through. This is mostly for long-form documentation, or working through ideas on paper first. I wouldn't suggest managing tasks via a notebook, it becomes too cumbersome and you may not always have your notebook on you when you need to check a todo (in an impromptu meeting, or if you think of something at the grocery store, etc).
Trello: This helps break down tasks and organizes which tasks / todos are left. Think of it more as project management, and don't try to document the world in Trello. Of course, whenever I do an expense claim I take pictures of the receipts and store them in trello in case I need to look them up again, but otherwise I don't store too much outside of basic tasks / todos. My only personal gripe is that Trello doesn't really offer Bitbucket integration (only Github), so referencing my Bitbucket issues on project boards can be somewhat tiresome. But specific features, issues, and tasks from Bitbucket projects do make it on Trello, and I move / archive / delete tasks based on how things end up getting implemented. Usually if I delete or archive a task, I leave a short comment (e.g. deleted in favour of doing X, or resolved via issue #Y on Bitbucket, with any specifics for that issue put into the issue tracker).
I've been trying my best to quantify things into tasks and just throw them on Trello, rather than have things scattered between my email inbox, Bitbucket issues, etc, that I'm currently working on. As for indices / an index, I don't really find it necessary. Most of the long-form stuff I care about is in my "current" notebook, and I can more or less figure out where other documentation is if I need to find it.