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Before you replace every pawn in the game with a new class, there's alternative methods you should probably look at. The replacement approach carries with it the potential for really bad conflicts with other mods.

Have you considered a ThingComp? Depending on how much code you've changed in the base class it may be possible to move the behavior out to a comp that gets added to pawns instead of replacing them.

You can also create a custom Tracker like those that hold the other aspects of pawn behavior (e.g. the HealthTracker or EquipmentTracker). This is a little more involved and has some overhead but you can guarantee that every pawn has one, which isn't necessarily possible with adding comps. You'd also have much more control over the tracker than the comp.

You'll definitely have to use Harmony of course, but realize that you can make any change to the vanilla code that you can think of with Harmony. You can replicate your entire modified class with Harmony if need be and it would play a lot nicer with other mods than changing the class entirely. More complex changes may require the use of the transpiler though, which can be difficult.

No Active/Different Incidents, except a few quests ..

AllowTool Produces this error when I try the mine connected ores option, which works in the old save as well.
[AllowTool][ERR] Exception while processing context menu action: System.IndexOutOfRangeException: Array index is out of range.
  at Verse.EdificeGrid.get_Item (IntVec3 c) [0x00000] in <filename unknown>:0
  at AllowTool.Context.MenuProvider_Mine.TryGetMineableAtPos (IntVec3 pos, Verse.Map map) [0x00000] in <filename unknown>:0
  at AllowTool.Context.MenuProvider_Mine.MineDesignationExpansionIsValid (IntVec3 cellFrom, IntVec3 cellTo, Verse.Map map) [0x00000] in <filename unknown>:0
  at AllowTool.Context.MenuProvider_Mine.FloodExpandDesignationType (Verse.DesignationDef designationDef, Verse.Map map, AllowTool.Context.InitialCandidateFilter initialFilter, AllowTool.Context.ExpansionCandidateFilter expansionFilter) [0x00000] in <filename unknown>:0
  at AllowTool.Context.MenuProvider_Mine.ContextMenuAction (Verse.Designator designator, Verse.Map map) [0x00000] in <filename unknown>:0
  at AllowTool.Context.BaseDesignatorMenuProvider.InvokeActionWithErrorHandling (AllowTool.Context.MenuActionMethod action, Verse.Designator designator) [0x00000] in <filename unknown>:0
Verse.Log:Error(String, Boolean)
HugsLib.Utils.ModLogger:Error(String, Object[])
AllowTool.Context.BaseDesignatorMenuProvider:InvokeActionWithErrorHandling(MenuActionMethod, Designator)
AllowTool.Context.<>c__DisplayClass24_0:<MakeMenuOption>b__1()
Verse.FloatMenuOption:Chosen(Boolean, FloatMenu)
RecipeIcons.FloatMenuOptionLeft:DoGUI(Rect, Boolean, FloatMenu)
Verse.FloatMenu:DoWindowContents(Rect)
Verse.<WindowOnGUI>c__AnonStorey0:<>m__0(Int32)
UnityEngine.GUI:CallWindowDelegate(WindowFunction, Int32, Int32, GUISkin, Int32, Single, Single, GUIStyle)

And on load I get this for every pawn

Exception while recalculating Aurora thought state for pawn Kristy: System.NullReferenceException: Object reference not set to an instance of an object
at RimWorld.ThoughtWorker_GameCondition.CurrentStateInternal (Verse.Pawn) <0x000ed>
at RimWorld.ThoughtWorker_Aurora.CurrentStateInternal (Verse.Pawn) <0x0003c>
at RimWorld.ThoughtWorker.CurrentState (Verse.Pawn) <0x0002f>
at (wrapper dynamic-method) RimWorld.SituationalThoughtHandler.TryCreateThought_Patch1 (object,RimWorld.ThoughtDef) <0x000f3>

Verse.Log:Error(String, Boolean)
RimWorld.SituationalThoughtHandler:TryCreateThought_Patch1(Object, ThoughtDef)
RimWorld.SituationalThoughtHandler:CheckRecalculateMoodThoughts()
RimWorld.SituationalThoughtHandler:AppendMoodThoughts(List`1)
RimWorld.ThoughtHandler:GetAllMoodThoughts(List`1)
Fixable_Mood_Debuffs_Alert.<>c:<AllPawnsWhoWantToMaster>b__8_0(Pawn)
System.Collections.Generic.List`1:FindAllStackBits(Predicate`1)
System.Collections.Generic.List`1:FindAll(Predicate`1)
Fixable_Mood_Debuffs_Alert.Unhappy_Pet_Owners_Alert:AllPawnsWhoWantToMaster()
Fixable_Mood_Debuffs_Alert.Unhappy_Pet_Owners_Alert:get_AllUnhappyPawns()
Fixable_Mood_Debuffs_Alert.Unhappy_Pet_Owners_Alert:GetReport()
RimWorld.Alert:get_Active()
RimWorld.AlertsReadout:AlertsReadoutUpdate()
RimWorld.UIRoot_Play:UIRootUpdate()
Verse.Root:Update_Patch1(Object)
Verse.Root_Play:Update_Patch1(Object)

=== EDIT ===

For better or worse, the small mod list ..

I knew it would be you who answers first 

There were so few mods with new incidents back then, I never encountered a problem like this.
And after two days search in the forums, I still could not find a fitting description.

I allready tried to compare the two savegames, but I did not have a clue what to look for.
But I have to confess, before the bug happened, I removed two permanent world conditions from the savegame, which were added by an incident mod. ( RimOverhaul )
Those were so stupidly unbalanced, that it was just no fun. I allready was in the middle of an Toxic Fallout Incident, when the Lean Atmosphere Incident happened. It added more radiation to the atmosphere and made the temperature switch between -90°C and +100°C in a matter of in game hours ... the extreme temperatures might have been an interaction with the mod that changes heat and cold waves.

Well now I remember why I should have made a backup of my save 

=== EDIT ===

also I play localized, non-Steam .. so no unexpected updates either.

Hi Razuhl, thank you for the mod

I would like to know if it is possible to implement in your mod what is asked in this post (time schedule for the food administration):

https://ludeon.com/forums/index.php?topic=49530.msg464374

maybe a new option like this:

"Restrict non starving colonists with mood above minor break threshold from eating"

Hey what did you do with the old SpaceDorf !!
I bet he would know that one of the mod's which add new world incident's would cause the problem.
Just try to identify which new world incident appear from the last working safegame.
Then try to identify the mod which add that one.

I think I botched my Savegame somehow, but I don't know how.

The Game runs without problems, except when I switch to the World Map.
The the Menu on the bottom of the screen goes missing.
The mouse cursor and the hex selector are still visible, but the tileinfo is not updated.
I can return to the colony view when I click on a colonist, but thats all.

The Debug Menu spams the following error when I load the World Map.

Root level exception in OnGUI(): System.NullReferenceException: Object reference not set to an instance of an object
  at RimWorld.Planet.WorldGlobalControls.WorldGlobalControlsOnGUI () [0x00000] in <filename unknown>:0
  at RimWorld.WorldInterface.WorldInterfaceOnGUI () [0x00000] in <filename unknown>:0
  at RimWorld.UIRoot_Play.UIRootOnGUI () [0x00000] in <filename unknown>:0
  at Verse.Root.OnGUI () [0x00000] in <filename unknown>:0
Verse.Log:Error(String, Boolean)
Verse.Root:OnGUI()

and this output when returning to the colony map

System.NullReferenceException: Object reference not set to an instance of an object
  at RimWorld.Planet.World.WorldPostTick () [0x00000] in <filename unknown>:0
Verse.Log:Error(String, Boolean)
RimWorld.Planet.World:WorldPostTick()
Verse.TickManager:DoSingleTick()
Verse.TickManager:TickManagerUpdate()
Verse.Game:UpdatePlay()
Verse.Root_Play:Update_Patch1(Object)

I run a lot of mods, but the sad thing is, when I load an older game of the same colony with the same Modlist the world map
still works.

The game is completed, so no you should not really expect any changes except bug fixes.

Luckily there is a vast modding surge that IMO has only gotten better over the past year.

I was wrong, enemy pawns on raid use main tree. Now I am thinking what is constant tree for.

You may want look at PawnGenerator class. And method called something like find-player-start-location (don't remember exactly) with return type Vector3.
You may create harmony prefix patch with return false to not call original method.

I love this game, for me is the best! But I am worry about future of this game, there wasn't any changes for a more than year:
Public   1.0.2059   Release   2018.10.17   Release 1.0
There will be some nice big or not big changes for this game soon? Thx for reply.