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Great! Whatever gets your job done.

Do you have by chance an idea how the rich-content plugins might work with markdown?

Tables could just be HTML, but stuff like Gnuplot diagrams or GraphViz graphs need to store their input data aswell as the actual rendered image.

Thanks for mentioning markor, I was searching for something similar! How do you sync your notebook between your phone and your computer, if you don't mind me asking?

Back when I was searching for a good note-taking system, each and everyone of them had one feature that I wanted that was missing. Zim Wiki was the first system I decided to stick with, and after 4+ years I never gravely missed anything. However, if you don't like organizing your stuff hierarchically, your experience might differ. Also, I kinda dig the desktop-centric approach. It feels more like a real tool than just some kind of "app".

Because it's written in python it is comparatively easy to extend and through its integrated web server you can serve up your notes with a custom design in no time.

Yes, that was Munich with its LiMux project.

Incidentally and possibly unrelated, the project was abandoned after Microsoft moved their headquarters back into Munich.