Refactor Waypoints and WaypointManager handling

Waypoints emit too many signals that other objects tie into, access should be thought out and reimplemented to reduce the number of "changed" signals, and simplify waypoint editing and access.

The issue names Waypoints and WaypointManager but provides no file paths, tests, or concrete completion criteria. Start by locating those implementations and mapping their current changed-signal connections, then identify the existing waypoint-editing behavior that must remain intact while the access and signal design is reconsidered.

Written by the indexing model from the issue text.