I love the interface of wikijs and easy to run with docker-compose.
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Dokuwiki is my choice.
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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
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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
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I use search both in the gui and with a cli tool, and both work great!
I want to second Dokuwiki. It is a step up from text files in a folder, easier to install and maintain than Jekyll (I am a big fan of Jekyll but have a deep-seated hate for Ruby). When compared to all the other wikis it is by far the easiest to install, maintain, and move to another server.
Dokuwiki is all text files and a version of markdown, the files can easily move to another markdown system.
Another vote for Dokuwiki. All flat files, and no db. Also can run as a portable app on Windows, so you can bring it to work on a thumb drive.
I recently created WipWiki to solve 3 of your 4 points, search could be easily added though if your interested in collaborating.
You can play around with the UI here: https://wiki.wip2p.com
TiddlyWiki is my jam. Everything in one single html file (though can be a little more complex than that if needed).
QOwnNotes (https://github.com/pbek/QOwnNotes) is what I use
single binary install, and if you already have md files you just point it at them and go... if you don't like it (even after you edited a few of your files with it), well your files are still there, still in markdown
give it a shot :)
For an actual wiki that does all the things a wiki is supposed to, it’s hard to beat dokuwiki.
If you want a desktop wiki (as opposed to a web app) you might like Zim.