Are there any IP blocking applications or firewalls that support IPv6?
The ones I know about (pgld, moblock (sunset?) , nfblock, iplist (looks old)) are only for IPv4.
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Uncomplicated Firewall (ufw) runs over IP tables and handles this very well.
sudo ufw deny from 2001:db8::/32 to any
Will deny all traffic from the IPv6 subnet 2001:db8::/32. You can also select ports and protocols to deny, if you need that granularity. As always, see the man page for additional options.
ufw is in the repos, so you can install it with
sudo apt-get install ufw.