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While PuTTY has had IPv6 support since 0.58, its handling of IPv6 literal addresses (e.g., ::1) still leaves something to be desired. In particular, there are various places where hostnames form part of a colon-delimited syntax (e.g., port-forwarding configuration); this interacts badly with IPv6 addresses containing colons.
PuTTY should consistently accept IPv6 literals in the square-bracket notation defined for URLs (in RFC3986) wherever it accepts a hostname.
Audit trail for this bug.