Ask HN: What tools do you use for note-taking, progress tracking and TODO lists?

I usually work on multiple projects at once, using several computers and phones and need to get better at tracking progress I made (for my personal purposes), managing TODO lists and taking personal notes.

I'm quite unorganised in this regard and I'm looking to change this so that I can finally stop worrying that I forgot about implementing a feature or that I forgot how I solved a particular problem a few months ago.

I need to obtain inner peace to be able to focus more on solving actual problems rather than living in fear over note-keeping.

My "system" so far is like this: I keep one Markdown file per computer I work on. Each file contains:

  - TODO lists for multiple projects

  - personal, general TODO lists (not related to particular projects)

  - my insights (regarding e.g. newly read papers or notes when learning new algorithms)

  - links to materials I find interesting and want to read later (papers, tutorials, links to HN :), etc.)

All of these MD files are unorganised (TODO lists for a single project can be found at multiple places in the file, interleaved between links and unrelated notes). I tried synchronising the MD files using Git, but that seemed like an overhead for me. I think I need something that does automatically save history and it would be nice to show the date and times when a note was taken (so that a graphs of my activity could be made over time - but this is not required).

I guess I would like to have a solution that not only synchronises across all platforms (Linux, macOS, Windows, iOS), but most importantly is secure as my notes can contain sensitive information. If there is an open-source solution for this problem, I have no problem with self-hosting such system.

How do you keep your notes/TODOs/track progress?