Make the necessary patches to make waypoints actually work?

src/SpaceWarp.Game/API/Game/Waypoints/Waypoint.cs

@@ -85,6 +85,11 @@ public WaypointState State
 
     private bool _isDestroyed;
 
+    /// <summary>
+    /// Whether or not this waypoint has been destroyed
+    /// </summary>
+    public bool IsDestroyed => _isDestroyed || _waypointObject is { _isDestroyed: true };
+
     private static long _nextID;
 
     /// <summary>
@@ -147,13 +152,17 @@ public Waypoint(double latitude, double longitude, double? altitudeFromRadius =
     /// <exception cref="Exception">Thrown if the waypoint was already destroyed</exception>
     public void Destroy()
     {
-        if (_isDestroyed)
+        if (IsDestroyed)
         {
             throw new Exception("Waypoint was already destroyed");
         }
 
-        _waypointObject.Destroy();
-        _waypointObject = null;
+        if (State == WaypointState.Visible)
+        {
+            _waypointObject.Destroy();
+            _waypointObject = null;
+        }
+
         _isDestroyed = true;
     }
 
@@ -168,7 +177,7 @@ public void Destroy()
     public void Move(double latitude, double longitude, double? altitudeFromRadius = null,
         [CanBeNull] string bodyName = null)
     {
-        if (_isDestroyed)
+        if (IsDestroyed)
         {
             throw new Exception("Waypoint was already destroyed");
         }
@@ -197,7 +206,7 @@ public void Move(double latitude, double longitude, double? altitudeFromRadius =
     /// <exception cref="Exception">Thrown if the waypoint is destroyed</exception>
     public void Rename([CanBeNull] string name = null)
     {
-        if (_isDestroyed)
+        if (IsDestroyed)
         {
             throw new Exception("Waypoint was already destroyed");
         }

src/SpaceWarp.Game/Modules/Game.cs

@@ -1,7 +1,14 @@
-using JetBrains.Annotations;
+using System.Reflection;
+using HarmonyLib;
+using JetBrains.Annotations;
 using KSP.Game;
 using KSP.Messages;
+using SpaceWarp.API.Assets;
 using SpaceWarp.API.Game.Messages;
+using SpaceWarp.API.Game.Waypoints;
+using UnityEngine;
+using ILogger = SpaceWarp.API.Logging.ILogger;
+using Object = UnityEngine.Object;
 
 namespace SpaceWarp.Modules;
 
@@ -11,9 +18,18 @@ namespace SpaceWarp.Modules;
 [UsedImplicitly]
 public class Game : SpaceWarpModule
 {
+
+    internal static ILogger Logger;
     /// <inheritdoc />
     public override string Name => "SpaceWarp.Game";
 
+    /// <inheritdoc />
+    public override void PreInitializeModule()
+    {
+        Logger = ModuleLogger;
+        Harmony.CreateAndPatchAll(typeof(Patches.MapPatches));
+    }
+
     /// <inheritdoc />
     public override void InitializeModule()
     {

src/SpaceWarp.Game/Patches/MapPatches.cs

@@ -0,0 +1,18 @@
+using HarmonyLib;
+using KSP.Map;
+using KSP.Sim;
+using KSP.Sim.impl;
+using UnityEngine;
+
+namespace SpaceWarp.Patches;
+
+[HarmonyPatch]
+internal static class MapPatches
+{
+    [HarmonyPatch(typeof(Map3DView), nameof(Map3DView.ProcessSingleMapItem))]
+    [HarmonyPrefix]
+    // ReSharper disable once InconsistentNaming
+    public static bool SkipBadItems(Map3DView __instance, MapItem item) =>
+        item.MapItemType != MapItemType.Waypoint ||
+        ((ISimulationModelMap)__instance.Game.UniverseModel).FromGlobalId(item.SimGUID) != null;
+}

src/SpaceWarp.Game/SpaceWarp.Game.csproj

@@ -13,5 +13,6 @@
     </ItemGroup>
     <ItemGroup Label="Project references">
         <ProjectReference Include="$(SolutionDir)/src/SpaceWarp.Core/SpaceWarp.Core.csproj" Private="false"/>
+        <ProjectReference Include="..\SpaceWarp.UI\SpaceWarp.UI.csproj" />
     </ItemGroup>
 </Project>