docs: record the pinentry theming fix in MIGRATION.md

The GPG PIN dialog was the last unthemed Qt6 app. pinentry-qt links Qt6
despite the name, but gpg-agent is spawned from .bashrc and reparented to
init, so it never inherits the QT_QPA_PLATFORMTHEME that Hyprland sets for
its own children, and every pinentry it spawns fell back to Fusion.

Also restructures the document: it was headed "phase 1 (rofi)" and now
covers more than rofi, so the phase is a section rather than the title.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015gbjA2bmswN8jyPDKzrvqe

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