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The gopass issue suggests using pinentry-gnome3 as a workaround.
What I found (strace -f -p <YK-AGENT PID>) is that although the gnome3 package is installed and is set as default, yubikey-agent still uses an alternative tool that fails to cooperate with gopass. I haven't found the root cause yet (gpgconf also refers to the correct tool), but this may be a much easier workaround than downgrading the tool esp. if some patches from unmerged PR's are applied...
Bug from v1.10.0
go-piv
Error Logs
yubikey-agent
gpgconf
Workaround
Archlinux
Related
gopasspw/gopass#1879
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