You should take a look at the diff from 5de9fd9bfa22 to c40d5914b57b and fix the mismerges. (In hgtk log, click on 5de9fd9bfa22 and then on "diff to second Parent". It's not quite as informative as gitk's merge diff view, but better than nothing.) For example, planet/Objects.c4d/Environment.c4d/Clouds.c4d/Script.c got a superflous function, planet/Parkour.c4f/Cavern.c4s/Script.c still has conflict markers, and I'm not sure why the noref branch should change a mesh and a skeleton.

Also, your conflict resolution in C4AulParse.cpp left case AB_PARN_SET: without it's break. (I've noticed that while trying to do the merge myself. Here's the diff to your version, complete with a new mismerge in C4AulParse.cpp that was automatically resolved by mercurial or kdiff3:
diff -r 5de9fd9bfa22 -r 84cc5f6d1848 planet/Objects.c4d/Environment.c4d/Clouds.c4d/Script.c
--- a/planet/Objects.c4d/Environment.c4d/Clouds.c4d/Script.c  Sun Aug 01 16:23:36 2010 +0100
+++ b/planet/Objects.c4d/Environment.c4d/Clouds.c4d/Script.c  Wed Aug 04 01:17:11 2010 +0200
@@ -1,27 +1,5 @@
/*-- Cloud Placer --*/

-<<<<<<< local
-//Great thanks to Maikel for the following function provided
-global func FindPosInMat(string sMat, int iXStart, int iYStart, int iWidth, int iHeight, int iSize)
-{
-  var iX, iY;
-  for(var i = 0; i < 500; i++)
-  {
-    iX = iXStart+Random(iWidth);
-    iY = iYStart+Random(iHeight);
-    if(GetMaterial(AbsX(iX),AbsY(iY))==Material(sMat) &&
-       GetMaterial(AbsX(iX+iSize),AbsY(iY+iSize))==Material(sMat) &&
-       GetMaterial(AbsX(iX+iSize),AbsY(iY-iSize))==Material(sMat) &&
-       GetMaterial(AbsX(iX-iSize),AbsY(iY-iSize))==Material(sMat) &&
-       GetMaterial(AbsX(iX-iSize),AbsY(iY+iSize))==Material(sMat)
-    ) {
-      return [iX, iY]; // Location found.
-    }
-  }
-  return 0; // No location found.
-}
-=======
->>>>>>> other
protected func Initialize()
{
   var iCount = LandscapeWidth()/65; //Determines how many clouds should be on a map
diff -r 5de9fd9bfa22 -r 84cc5f6d1848 planet/Parkour.c4f/Cavern.c4s/Script.c
--- a/planet/Parkour.c4f/Cavern.c4s/Script.c  Sun Aug 01 16:23:36 2010 +0100
+++ b/planet/Parkour.c4f/Cavern.c4s/Script.c  Wed Aug 04 01:17:11 2010 +0200
@@ -19,12 +19,8 @@
     if (!(pos = FindPosInMat("Tunnel", 0, LandscapeHeight() - d - 80, LandscapeWidth(), 80, 20)) || !Random(3))
       pos = FindPosInMat("Sky", 0, LandscapeHeight() - d - 80, LandscapeWidth(), 80, 20);
     else
-<<<<<<< local
-      mode = mode | RACE_CP_Respawn;
+      mode = mode | PARKOUR_CP_Respawn;
     x = pos[0]; y = pos[1];
-=======
-      mode = mode | PARKOUR_CP_Respawn;
->>>>>>> other
     // All checkpoints ordered.
     mode = mode | PARKOUR_CP_Ordered;
     goal->AddCheckpoint(x, y, mode);
diff -r 5de9fd9bfa22 -r 84cc5f6d1848 planet/System.c4g/Commits.c
--- a/planet/System.c4g/Commits.c  Sun Aug 01 16:23:36 2010 +0100
+++ b/planet/System.c4g/Commits.c  Wed Aug 04 01:17:11 2010 +0200
@@ -377,4 +377,5 @@
     }
   }
   return 0; // No location found.
-}
\ No newline at end of file
+}
+
diff -r 5de9fd9bfa22 -r 84cc5f6d1848 src/C4Version.h
--- a/src/C4Version.h  Sun Aug 01 16:23:36 2010 +0100
+++ b/src/C4Version.h  Wed Aug 04 01:17:11 2010 +0200
@@ -42,7 +42,7 @@
#define C4XVERBUILD           2
#define C4VERSIONBUILDNAME    "Cerulean"
#define C4VERSIONEXTRA        "Beta"
-#define C4REVISION            "8b0d67bef90e+c40d5914b57b+"
+#define C4REVISION            "25a791c06fff+"

#define C4ENGINEINFO          "OpenClonk Reborn Beta"
#define C4ENGINEINFOLONG      "OpenClonk Reborn Beta (Cerulean)"
diff -r 5de9fd9bfa22 -r 84cc5f6d1848 src/game/object/C4DefGraphics.cpp
--- a/src/game/object/C4DefGraphics.cpp  Sun Aug 01 16:23:36 2010 +0100
+++ b/src/game/object/C4DefGraphics.cpp  Wed Aug 04 01:17:11 2010 +0200
@@ -1084,7 +1084,7 @@
       }

       C4Value value;
-      pDef->GetPropertyVal(P_MeshTransformation, &value);
+      pDef->GetPropertyVal(P_MeshTransformation, value);
       StdMeshMatrix matrix;
       if (C4ValueToMatrix(value, &matrix))
         lpDDraw->SetMeshTransform(&matrix);
diff -r 5de9fd9bfa22 -r 84cc5f6d1848 src/script/C4AulExec.cpp
--- a/src/script/C4AulExec.cpp  Sun Aug 01 16:23:36 2010 +0100
+++ b/src/script/C4AulExec.cpp  Wed Aug 04 01:17:11 2010 +0200
@@ -204,7 +204,8 @@
         break;
       case AB_PARN_SET:
         pCurCtx->Pars[pCPos->Par.i] = pCurVal[0];
-     
+        break;
+
       case AB_PARN_CONTEXT:
         PushValue(AulExec.GetContext(AulExec.GetContextDepth()-2)->Pars[pCPos->Par.i]);
         break;
diff -r 5de9fd9bfa22 -r 84cc5f6d1848 src/script/C4AulExec.h
--- a/src/script/C4AulExec.h  Sun Aug 01 16:23:36 2010 +0100
+++ b/src/script/C4AulExec.h  Wed Aug 04 01:17:11 2010 +0200
@@ -154,7 +154,7 @@
     }
     else if (pStructure->ConvertTo(C4V_PropList) && pStructure->GetType() != C4V_Any)
     {
-      if (!pIndex->ConvertTo(C4V_String) || !pIndex->_getStr())
+      if (!pIndex->ConvertTo(C4V_String))
         throw new C4AulExecError(pCurCtx->Obj, FormatString("proplist access: index of type %s, string expected!", pIndex->GetTypeName()).getData());
       return C4V_PropList;
     }
diff -r 5de9fd9bfa22 -r 84cc5f6d1848 src/script/C4AulParse.cpp
--- a/src/script/C4AulParse.cpp  Sun Aug 01 16:23:36 2010 +0100
+++ b/src/script/C4AulParse.cpp  Wed Aug 04 01:17:11 2010 +0200
@@ -1028,12 +1028,12 @@
   case AB_NIL:
   case AB_VARN:
   case AB_PARN:
-  case AB_PARN_CONTEXT:
-  case AB_VARN_CONTEXT:
   case AB_LOCALN:
   case AB_GLOBALN:
   case AB_DUP:
     return 1;
+  case AB_PARN_CONTEXT:
+  case AB_VARN_CONTEXT:

   case AB_Pow:
   case AB_Div:
@@ -1994,11 +1994,9 @@
       if (pFunc && (Type == PARSER))
       {
         C4V_Type to = pFunc->GetParType()[size];
-        // pFunc either was the return value from a GetFirstFunc-Call or
-        // pFunc is the only function that could be called, so this loop is superflous
-        C4AulFunc * pFunc2 = pFunc;
-        while ((pFunc2 = a->Engine->GetNextSNFunc(pFunc2)))
+        {
           if (pFunc2->GetParType()[size] != to) to = C4V_Any;
+        }
         C4V_Type from;
         switch ((a->CPos-1)->bccType)
         {
diff -r 5de9fd9bfa22 -r 84cc5f6d1848 src/script/C4Value.h
--- a/src/script/C4Value.h  Sun Aug 01 16:23:36 2010 +0100
+++ b/src/script/C4Value.h  Wed Aug 04 01:17:11 2010 +0200
@@ -60,7 +60,6 @@
   // cheat a little - assume that all members have the same length
   operator void * () { return Obj; }
   operator const void * () const { return Obj; }
-  bool operator== (C4V_Data b) { return Obj == b.Obj; }
   C4V_Data &operator = (void *p) { Obj = reinterpret_cast<C4Object *>(p); return *this; }
};


What are you doing in UK, btw?

If I see this correctly, you forgot at least:
1. parts of the System.c4g (I remember that there was at least one function in Colors.c that used references)
2. to update the documentation