I'm a bit worried that, as far as I see, the Syncthing protocol doesn't really allow having servers/peers that don't see plain-text. (Since I think it mostly just uses TLS to keep things secret from eavesdroppers.) I've always been looking for an open source Dropbox-like that allows having storage that only sees ciphertext (despite the fact that it would require a little key management from the user, which I think is a usability challenge, but one that can be overcome).
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BitTorrent Sync has functionality for generating "encrypted secrets" using the developer API. It is possible to deliver a secret key to a peer which only allows for that peer to access encrypted versions of the folder content.
did you take a look at sparkleshare,
it's kind of a dropboxreplacement based on git.
Last time i checkt it was possible to enable ciphertext storage ( https://github.com/hbons/SparkleShare/wiki/Client-Side-Encry... ) .
Look at boxcryptor (works with dropbox)