Works for me:
elajoie@skylake:~/fairphone_os$ repo init -u ssh://code.fairphone.com:29418/fp2-dev/manifest -b fp2-sibon
Your identity is: Eric Lajoie email@example.com
If you want to change this, please re-run ‘repo init’ with --config-name
repo has been initialized in /home/elajoie/fairphone_os
Maybe line 46 in your .ssh/known_hosts file needs to be removed and you can add the one below:
[code.fairphone.com]:29418 ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAAAgQCTQ1o0jhAfkLvMbXwUXLGdPWZ7VvyFLaMTxT6/LmiLqg20E/6oKEw/2Hw5mINhpFRvd7BGZ7n8FieXqJ1Z+FIsAyZA90e5tpqAihRU9Lmh2s4IeADRxEv0gLxiVvkc7DmcCIZM6SDEKq5xuZZqSvSy/VQxxfGRfUt6PykVRLw7jw==
Also can you confirm you did a ssh-add .ssh/id_rsa on your private key as I had same issue and it started working after I added it.