There are also a lot of mcp agents for Joplin: https://discourse.joplinapp.org/t/ai-agents-and-joplin/46168 Dare I say, another, more popular, note taking app for you and your agents.

I really like it as I run a webdav service and can read/write and sync notes between multiple Mac desktops and Android. Encrypted while I am at it.

Markdown native.