I too have heard about syncthing for the first time today but from a different submission[0] you might care to be aware of.

Although, I realize Android != Kindle's OS, so I'm not sure how much concern there should be.

[0]: https://news.ycombinator.com/item?id=46184730 "Syncthing-Android have had a change of owner/maintainer"

If you have calibre, just turn on the wireless connection and have your Koreader connect to it.

https://github.com/koreader/koreader/wiki/calibre

Personally I'm most fond of Calibre + Calibre-Web, which masquerades as the Kobo Store and lets you use the built-in Kobo syncing mechanisms with your Calibre library instead of having to do it all within Koreader.