Our familiar old file-copying friends SSH, SCP, and Rsync are all IPv6-ready, which is the good news. The bad news is they have syntax quirks which you must learn to make them work. Before we get into the details, though, you might want to review the previous installments in our meandering IPv6 series:
Remote terminal application that allows roaming, supports intermittent connectivity, and provides intelligent local echo and line editing of user keystrokes.
Mosh is a replacement for SSH. It's more robust and responsive, especially over Wi-Fi, cellular, and long-distance links.
Mosh is free software, available for GNU/Linux, FreeBSD, and Mac OS X.