I didn't keep track of what changed.

Source/HoloDeck.cs

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+/*
+ * The MIT License (MIT)
+ *
+ * Copyright (c) 2015 Alexander Taylor
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ * THE SOFTWARE.
+ */
+
+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using System.Reflection;
+
+using UnityEngine;
+
+using HoloDeck.SceneModules;
+
+namespace HoloDeck
+{
+    // We want to load in all relevant game scenes, and be applied to all games.
+    [KSPScenario(ScenarioCreationOptions.AddToAllGames, new GameScenes[] { GameScenes.SPACECENTER, GameScenes.EDITOR, GameScenes.FLIGHT, GameScenes.TRACKSTATION })]
+    class HoloDeck : ScenarioModule
+    {
+        // Tag for marking debug logs with
+        private const string TAG = "HoloDeck.HoloDeck";
+
+        // This class is a singleton, as much as Unity will allow. 
+        // There is probably a better way to do this in a Unity-like way,
+        // But I don't know it. 
+        public static HoloDeck instance;
+
+        // This is a flag for marking a save as 'dirty'. Any flag with this flag 
+        // that enters SPACECENTER, EDITOR, or TRACKSTATION will be immediately reset
+        [KSPField(isPersistant = true)]
+        public bool SimulationActive = false;
+
+        // This is our entry point
+        void Start()
+        {            
+            // update the singleton
+            instance = this;
+
+            // Reload to pre-sim if we are in the wrong scene.
+            if (HighLogic.LoadedScene != GameScenes.FLIGHT)
+            {
+                HoloDeck.Deactivate(GameScenes.SPACECENTER);
+            }
+
+            // Deploy scene-specific modules, for GUI hijacking and similar logic
+            switch (HighLogic.LoadedScene)
+            {
+                case GameScenes.FLIGHT:
+                    gameObject.AddComponent<FlightModule>();
+                    break;
+                case GameScenes.EDITOR:
+                    gameObject.AddComponent<EditorModule>();
+                    break;
+            }
+
+            // If the sim is active, display the tell-tale
+            SimulationNotification(SimulationActive);
+        }
+
+        // This is called when the script is destroyed.
+        // This is honestly probably not necessary, but better safe than sorry
+        void Destroy()
+        {
+            SimulationNotification(false); 
+            instance = null;
+        }
+
+        // Activates the Simulation. Returns the success of the activation.
+        public static bool Activate()
+        {
+            // for recording save status, not sure what this string actually is tbh
+            string save = null;
+
+            // Make sure the instance actually exists. I can't imagine this ever failing, but NREs are bad.
+            if (instance != null)
+            {   
+                // We create the pre-sim save.
+                save = GamePersistence.SaveGame("HoloDeckRevert", HighLogic.SaveFolder, SaveMode.OVERWRITE);
+
+                // Mark the existing save as dirty.
+                HoloDeck.instance.SimulationActive = true;
+
+                // Record the scene we are coming from
+                HoloDeckShelter.lastScene = HighLogic.LoadedScene;
+
+                if (HoloDeckShelter.lastScene == GameScenes.EDITOR)
+                {
+                    HoloDeck.OnLeavingEditor(EditorDriver.editorFacility, EditorLogic.fetch.launchSiteName);
+                }
+
+                // Start the tell-tale
+                HoloDeck.instance.SimulationNotification(true);
+            }
+
+            return save != null ? true : false;
+        }
+
+        // Deactivates the simulation. Success is destructive to the plugin state,
+        // so... no return value
+        public static void  Deactivate(GameScenes targetScene)
+        {
+            // This method only does something if the sim is active.
+            if (HoloDeck.instance.SimulationActive)
+            {
+                // Weird bug can be intorduced by how KSP keeps around KSPAddons until it decides to destroy
+                // them. We need to preempt this so extraneous behavior isn't observed
+                FlightModule[] flightModules = GameObject.FindObjectsOfType(typeof(FlightModule)) as FlightModule[];
+                EditorModule[] editorModules = GameObject.FindObjectsOfType(typeof(EditorModule)) as EditorModule[];
+
+                foreach (FlightModule flightModule in flightModules)
+                {
+                    DestroyImmediate(flightModule);
+                }
+
+                foreach (EditorModule editorModule in editorModules)
+                {
+                    DestroyImmediate(editorModule);
+                }
+
+                // Ok, here is where this is tricky. We can't just directly load the save, we need to 
+                // load the save into a new Game object, re-save that object into the default persistence,
+                // and then change the scene. Weird shit, right? This is actually how the vanilla quickload
+                // works!
+                Game newGame = GamePersistence.LoadGame("HoloDeckRevert", HighLogic.SaveFolder, true, false);
+                GamePersistence.SaveGame(newGame, "persistent", HighLogic.SaveFolder, SaveMode.OVERWRITE);
+                newGame.startScene = targetScene;
+
+                // This has to be before... newGame.Start()
+                if (targetScene == GameScenes.EDITOR)
+                {
+                    newGame.editorFacility = HoloDeckShelter.lastEditor;
+                }
+
+                newGame.Start();
+                HoloDeck.instance.SimulationActive = false;
+
+                // ... And this has to be after. <3 KSP
+                if (targetScene == GameScenes.EDITOR)
+                {
+                    EditorDriver.StartupBehaviour = EditorDriver.StartupBehaviours.LOAD_FROM_CACHE;
+                    ShipConstruction.ShipConfig = HoloDeckShelter.lastShip;
+                }
+            }
+        }
+
+        // This method should be called before activating the simulation directly from an editor, and allows 
+        // QOL improvements (like returning to that editor correctly, and automatically clearing the launch site)
+        // Either of these values can be null, if you want to do that for some reason
+        public static void OnLeavingEditor(EditorFacility facility, string launchSiteName) 
+        {
+            // clear the launchpad.
+            if (launchSiteName != null)
+            {
+                List<ProtoVessel> junkAtLaunchSite = ShipConstruction.FindVesselsLandedAt(HighLogic.CurrentGame.flightState, launchSiteName);
+
+                foreach (ProtoVessel pv in junkAtLaunchSite)
+                {
+                    HighLogic.CurrentGame.flightState.protoVessels.Remove(pv);
+                }
+            }
+
+            if (facility != EditorFacility.None)
+            {
+                HoloDeckShelter.lastEditor = facility;
+            }
+
+            HoloDeckShelter.lastShip = ShipConstruction.ShipConfig;
+        }
+
+        // This is in here instead of GUI, because this isn't an 'implementation detail'
+        // If some other mod uses sim mode for some reason, I still want this displayed.
+        private void SimulationNotification(bool state)
+        {
+            if (HighLogic.LoadedScene == GameScenes.FLIGHT)
+            {
+                switch (state)
+                {
+                    case true:
+                        InvokeRepeating("DoSimulationNotification", 0.1f, 1.0f);
+                        break;
+
+                    case false:
+                        CancelInvoke("DoSimulationNotification");
+                        break;
+                }
+            }
+        }
+
+        private void DoSimulationNotification()
+        {
+            ScreenMessages.PostScreenMessage("Simulation Active", 1.0f, ScreenMessageStyle.LOWER_CENTER);
+        }
+    }
+}

Source/HoloDeck.csproj

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+<?xml version="1.0" encoding="utf-8"?>
+<Project ToolsVersion="12.0" DefaultTargets="Build" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
+  <Import Project="$(MSBuildExtensionsPath)\$(MSBuildToolsVersion)\Microsoft.Common.props" Condition="Exists('$(MSBuildExtensionsPath)\$(MSBuildToolsVersion)\Microsoft.Common.props')" />
+  <PropertyGroup>
+    <Configuration Condition=" '$(Configuration)' == '' ">Debug</Configuration>
+    <Platform Condition=" '$(Platform)' == '' ">AnyCPU</Platform>
+    <ProjectGuid>{8C5539DD-396B-4084-892E-8F1901E51584}</ProjectGuid>
+    <OutputType>Library</OutputType>
+    <AppDesignerFolder>Properties</AppDesignerFolder>
+    <RootNamespace>HoloDeck</RootNamespace>
+    <AssemblyName>HoloDeck</AssemblyName>
+    <TargetFrameworkVersion>v3.5</TargetFrameworkVersion>
+    <FileAlignment>512</FileAlignment>
+  </PropertyGroup>
+  <PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Debug|AnyCPU' ">
+    <PlatformTarget>AnyCPU</PlatformTarget>
+    <DebugSymbols>true</DebugSymbols>
+    <DebugType>full</DebugType>
+    <Optimize>false</Optimize>
+    <OutputPath>bin\Debug\</OutputPath>
+    <DefineConstants>DEBUG;TRACE</DefineConstants>
+    <ErrorReport>prompt</ErrorReport>
+    <WarningLevel>4</WarningLevel>
+  </PropertyGroup>
+  <PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Release|AnyCPU' ">
+    <PlatformTarget>AnyCPU</PlatformTarget>
+    <DebugType>pdbonly</DebugType>
+    <Optimize>true</Optimize>
+    <OutputPath>bin\Release\</OutputPath>
+    <DefineConstants>TRACE</DefineConstants>
+    <ErrorReport>prompt</ErrorReport>
+    <WarningLevel>4</WarningLevel>
+  </PropertyGroup>
+  <PropertyGroup>
+    <StartupObject />
+  </PropertyGroup>
+  <ItemGroup>
+    <Reference Include="Assembly-CSharp">
+      <HintPath>..\..\..\..\..\..\..\Games\Kerbal Space Program\KSP_Data\Managed\Assembly-CSharp.dll</HintPath>
+    </Reference>
+    <Reference Include="Assembly-CSharp-firstpass">
+      <HintPath>..\..\..\..\..\..\..\Games\Kerbal Space Program\KSP_Data\Managed\Assembly-CSharp-firstpass.dll</HintPath>
+    </Reference>
+    <Reference Include="UnityEngine">
+      <HintPath>..\..\..\..\..\..\..\Games\Kerbal Space Program\KSP_Data\Managed\UnityEngine.dll</HintPath>
+    </Reference>
+  </ItemGroup>
+  <ItemGroup>
+    <Compile Include="SceneModules\EditorModule.cs" />
+    <Compile Include="SceneModules\FlightModule.cs" />
+    <Compile Include="HoloDeck.cs" />
+    <Compile Include="HoloDeckShelter.cs" />
+  </ItemGroup>
+  <Import Project="$(MSBuildToolsPath)\Microsoft.CSharp.targets" />
+  <PropertyGroup>
+    <PostBuildEvent>xcopy /Y $(TargetPath) $(TargetDir)..\..\..\GameData\Fingerboxes\HoloDeck\Plugins\</PostBuildEvent>
+  </PropertyGroup>
+  <!-- To modify your build process, add your task inside one of the targets below and uncomment it. 
+       Other similar extension points exist, see Microsoft.Common.targets.
+  <Target Name="BeforeBuild">
+  </Target>
+  <Target Name="AfterBuild">
+  </Target>
+  -->
+</Project>

Source/HoloDeck.sln

@@ -0,0 +1,28 @@
+
+Microsoft Visual Studio Solution File, Format Version 12.00
+# Visual Studio 2013
+VisualStudioVersion = 12.0.31101.0
+MinimumVisualStudioVersion = 10.0.40219.1
+Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "HoloDeck", "HoloDeck.csproj", "{8C5539DD-396B-4084-892E-8F1901E51584}"
+EndProject
+Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "FingerboxLib", "..\..\FingerboxLib\Source\FingerboxLib.csproj", "{6AE0BA91-9473-43E6-980D-C7B04CCAEB45}"
+EndProject
+Global
+	GlobalSection(SolutionConfigurationPlatforms) = preSolution
+		Debug|Any CPU = Debug|Any CPU
+		Release|Any CPU = Release|Any CPU
+	EndGlobalSection
+	GlobalSection(ProjectConfigurationPlatforms) = postSolution
+		{8C5539DD-396B-4084-892E-8F1901E51584}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
+		{8C5539DD-396B-4084-892E-8F1901E51584}.Debug|Any CPU.Build.0 = Debug|Any CPU
+		{8C5539DD-396B-4084-892E-8F1901E51584}.Release|Any CPU.ActiveCfg = Release|Any CPU
+		{8C5539DD-396B-4084-892E-8F1901E51584}.Release|Any CPU.Build.0 = Release|Any CPU
+		{6AE0BA91-9473-43E6-980D-C7B04CCAEB45}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
+		{6AE0BA91-9473-43E6-980D-C7B04CCAEB45}.Debug|Any CPU.Build.0 = Debug|Any CPU
+		{6AE0BA91-9473-43E6-980D-C7B04CCAEB45}.Release|Any CPU.ActiveCfg = Release|Any CPU
+		{6AE0BA91-9473-43E6-980D-C7B04CCAEB45}.Release|Any CPU.Build.0 = Release|Any CPU
+	EndGlobalSection
+	GlobalSection(SolutionProperties) = preSolution
+		HideSolutionNode = FALSE
+	EndGlobalSection
+EndGlobal

Source/HoloDeckShelter.cs

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+using System;
+using System.Collections.Generic;
+using System.Linq;
+using System.Text;
+using UnityEngine;
+
+namespace HoloDeck.SceneModules
+{
+    // This class is a place to stick data that will not be destroyed by HoloDeck.Deactivate(). 
+    [KSPAddon(KSPAddon.Startup.Instantly, true)]
+    class HoloDeckShelter : MonoBehaviour
+    {
+        // Editor stuff
+        public static EditorFacility lastEditor = EditorFacility.None;
+        public static ConfigNode lastShip = null;
+
+        public static GameScenes lastScene;
+
+        void Awake()
+        {
+            DontDestroyOnLoad(this);
+        }
+    }
+}