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I use org-mode (in spacemacs), folder synchronized on some cloud, private notes GPG encrypted. For me it's more than perfect. I always find what I am looking for immediately, org-mode is useful in lots of other use cases, emacs has been around for a long time and I trust will stay for the rest of my life...

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I second org-mode. Previously I was using OneNote but that is limited to Windows, and on Linux I need to be always online to use the web interface.

To add one more use case: I was thinking of creating flash cards and came across org-dribble which provides the entire functionality of creating and revising flash cards using Supermemo method.

When it comes to note-taking and organising, org-mode is an excellent choice.

I think it is org-drill.

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