Selfhosted
A place to share alternatives to popular online services that can be self-hosted without giving up privacy or locking you into a service you don't control.
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Joplin
+1 for Joplin. Sync via webdav-server (nginx, nextcloud) or their sync server. Works like a charm.
I installed joplin, and while it doesn't have flat file structure, I think this is the way to go. It's easy enough to create backups through the UI.
Does everyone pay for Joplin or is there a way to get it to work for free?
You can use Joplin without Paying. You only need to pay for Joplin Cloud for syncing. But you can use a selfhosted Joplin Server or Webdav to sync you notes without it.