We use strong cryptographic hashes to make sure the version that was announced is the version you pull, even if the file was requested from a different peer.
Files are transferred either
This is the same mechanism as if you sent a file through your IM client.
All XMPP communication is TLS encrypted.
You may use your own XMPP server to keep your data internal.
In this case, the connection is AES encrypted.
In this case, the connection is AES encrypted.
These high encryption standards are common place in banking and data encryption. There is no snake oil here, we use well-tested, proven and established mechanisms.
Just continue to use your current backup mechanism as is to avoid the tears of accidental deletes, pulls, overrides, etc.
Also, Jake does not provide disk or file encryption, as this would be a stupid idea. There are other programs you can use in combination with Jake to achieve protection from data theft (e.g. stolen laptop).