Technology
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My biggest issue with all these Markdown editors is that the format is text only, forcing other files to be stored independently. It does not support embedded pictures, formulas, etc.
My perfect option uses some format that would allow text, pictures, audio and video, optional LaTeX formatting all in one file, and wouldn't be constrained to a single application that can run it all. At least some apps supporting it should be in a note-taking layout, not a standard office program.
Mobile support would be a banger, too, but is optional.
Essentially, I want a OneNote-like experience without walled garden, bundled in a way that would allow it to be painlessly exported into several other pieces of software, available on Linux.
Any ideas on that?
Obsidian to an extent? Maybe? Idk.
Not really, still MD-based :(
Closest to that were Trilium and Zettlr, but again, they store media separately and address it in inconvenient ways.
How so?
I configured Obsidian to throw all media files in one directory.
All files are referenced by a common picture link

Thanks! Will check it out
P.S. Seems more like a general purpose editor with a twist, though, and not a solid note-taking solition upon the first glance. Thanks for the recommendation anyway!
Well, you can use it as such, storing the notes locally with the corresponding title. You'll find a lot more on the SSuite, maybe there you'll find something els which may serve you, anyway good to bookmark it, it's pretty usefull.
But I also remember another app, an old Gem, OpenSource which may fullfit your needs, it's a very powerfull tree style note taking app, rich text format and if you need, also syntax highlighting for programming scripts. (Windows, Linux) (.rtf, .txt, scripts)
https://github.com/giuspen/cherrytree
https://www.giuspen.net/cherrytree/#downl
Appears to be, yep