flathub: move to the latest GNOME runtime (48 is end-of-life) #1579

Part of #1060. Reviewer: "It's not the latest runtime." Linter: runtime-is-eol-org.gnome.Platform-48 (error), runtime-update-available-to-org.gnome.Platform-51 (warning).

Rules: the runtime "must be the latest version at that time of submission"; "Submissions using an end-of-life runtime ... will not be accepted."

Work

• Switch runtime-version to the latest GNOME runtime offered by the linter at submission time
• Check GTK 3 / libsecret / libayatana-appindicator (if used) availability in that runtime
• Re-test: window, theming, file chooser, secrets, SSH tunnels, MCP server
• Re-run flatpak-builder-lint manifest