chore: prepare 3.1.0 release (#6125)

* docs: add 3.1 entries to the changelog

Assisted-by: ClaudeCode:claude-opus-5
Signed-off-by: Henry Schreiner <henryfs@princeton.edu>

* chore: prepare 3.1.0 release

Assisted-by: ClaudeCode:claude-opus-5

* [skip ci] Change release date to August 4, 2026

* docs: add #6127 entry and set release date to August 6, 2026

Assisted-by: ClaudeCode:claude-opus-5

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Signed-off-by: Henry Schreiner <henryfs@princeton.edu>
Co-authored-by: Ralf W. Grosse-Kunstleve <rwgkio@gmail.com>