[StudentWeis]

Summary

Clearing the global activation shortcut now disables it through save and restart. Reopening or refocusing a popup preserves active confirmation dialogs and their keyboard focus, and the AgentBay Linux recipe explicitly exercises X11.

Linked Issue

Closes #302

Changes

• Preserve explicitly empty shortcut candidates, show the cleared candidate, and retain disabled shortcuts during startup validation. Reuse the shared settings persistence path.
• Keep confirmation state, focus and the underlying panel intact during activation. Update windows without mutably borrowing Root before dialog queries.
• Remove inherited Wayland variables from X11 test clients and verify the popup's X11 window against its process ID.

Testing

• scripts/precheck.sh passes locally: 748 Rust tests, 83 Python tests, Clippy, resource checks, dependency boundaries and rustdoc.
• New / updated tests cover the change. The shortcut clear/save/reload and dialog reactivation assertions failed before their fixes and pass afterward. Window tests cover hotkey, tray, pinned refocus and transient recreation paths.
• Markdown validation, Bash syntax validation and the documented X11 child environment check pass.
• Native cross-platform GUI acceptance was not run. UI coverage uses real GPUI components on the headless test platform; the hotkey registration manager is isolated.
• The existing third-party block 0.1.6 future-compatibility warning remains.

Self-Check

• PR title follows Conventional Commits
• No hardcoded user-facing strings — existing i18n keys are reused
• Errors defined with thiserror — no new error types
• No unrelated changes mixed in