I'm actually not sure if it's open source (probably not?) but I love Obsidian. You can cross-reference notes as much as you want, so that you could - for instance - take an insight from soil biology and link it to something happening in your local community AND to a note about sheep fodder AND to a series of notes about your compost experiments AND to your 2024 pasture plans - without ever moving the individual notes into folders.

I know that you asked about segregation, and Obsidian can do that (folders, vaults) but the magic of cross-pollinating your knowledge and ideas is that you don't have to do that unless you have a particularly compelling reason to. You can avoid creating silos for ideas.

Also the notes live on your device in a simple format (I don't remember what it's called - markdown text, maybe?)

Awesome Privacy has a section on note taking software:

https://github.com/pluja/awesome-privacy?tab=readme-ov-file#notes-and-tasks

Out of these I can only personally vouch for Obsidian - I've been meaning to try out Logseq as well.