I had this issue with Windows. This is how I solved it:
When I installed Nitrous.io Desktop the application scanned my computer for existing rsa keys. I believe it found them; however, I had set up my private key to have a passphrase. It seems that the passphrase was the issue with the file Sync. The "Shell" connection worked properly but it prompted me for my passphrase before connecting; this gave me a clue.
This is how I solved it:
- Go to Nitrous.io Desktop Preferences by right clicking on the notification area icon.
- Check the rsa_key files being used.
- Find and delete the old rsa keys files.
- Click on rescan
- Generate new SSH keys from within the Nitrous.io Desktop App
- Register them.
- Restart the Nitrous App.
- Syncing should be working now.