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On desktops with no tray host (stock GNOME), "Keep running in the tray" hid the window with no icon to bring it back. Ask the desktop app (has_tray_host); without a tray, say so, focus "Quit when I close the window", and offer "Keep running in the background" as the secondary choice. Older desktop builds keep the current dialog. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_017PCb59uY3UKqDqt7B6hzd5