This. This is exactly what I do. And it for both my lab which is my side hustle, and my big boy job. Its perfect!

Dokuwiki is my choice.

1. There is no database, all flat file just in folders, love this. When my infrastructure is down, at least I can still get to my notes so I can fix it

2. Its markdown but not exact markdown, but no DB makes it worth that pain. You can for sure edit via vi, finding the files is a little harder though

3. I use search both in the gui and with a cli tool, and both work great!