Edit: I realized everyone was responding to top comment, removed long winded rambling about my personal Linux journey.
I 100% second note taking - my personal favorite is ObsidianMD.
I used Joplin for many months, with WebDAV (koofr)/e2e setup for sync, till I discovered ObsidianMD.
Now: all my notes are in markdown/plantuml/mermaid/Obsidian canvas/drawio, managed primarily by ObsidianMD, but occasionally on vscode for special use cases (plantuml diagram editing… vscode flow is better). I use obsidian git to sync to my git repo across my machines. Still love Joplin in a pinch (mobile app on occasion) though.