Index: trunk/ppStack/src/ppStackSources.c
===================================================================
--- trunk/ppStack/src/ppStackSources.c	(revision 18356)
+++ trunk/ppStack/src/ppStackSources.c	(revision 18382)
@@ -17,4 +17,5 @@
     psArray *sources;                   // Sources within region
     psVector *indices;                  // Indices from tree to sources
+    psArray *duplicates;                // Duplicate sources (from overlaps)
     psTree *tree;                       // kd tree with sources
 } ppStackSourceList;
@@ -45,4 +46,5 @@
     psFree(list->sources);
     psFree(list->indices);
+    psFree(list->duplicates);
     psFree(list->tree);
 }
@@ -130,5 +132,6 @@
 // Extend a list of sources
 bool ppStackSourceListExtend(ppStackSourceList *list, // List to extend
-                             const psArray *newSources // Sources to add
+                             const psArray *newSources, // Sources to add
+                             const psArray *newDups // Duplicate sources to add
     )
 {
@@ -136,19 +139,32 @@
     psAssert(newSources, "Must be given sources");
 
-    psArray *oldSources = list->sources;// Old list of sources
-    long numOld = oldSources->n;        // Number of old sources
-    long numNew = newSources->n;        // Number of new sources
-
-    list->sources = oldSources = psArrayRealloc(oldSources, numOld + numNew);
-    for (long i = 0; i < numNew; i++) {
-        psArrayAdd(oldSources, 1, newSources->data[i]);
-    }
-    psFree(list->tree);
-
-    psVector *x = NULL, *y = NULL;      // Source coordinates
-    stackSourcesParse(&list->bounds, &x, &y, &list->indices, list->sources);
-    list->tree = psTreePlant(2, SOURCES_MAX_LEAF, x, y); // kd Tree with sources
-    psFree(x);
-    psFree(y);
+    {
+        psArray *oldSources = list->sources;// Old list of sources
+        long numOld = oldSources->n;        // Number of old sources
+        long numNew = newSources->n;        // Number of new sources
+
+        list->sources = oldSources = psArrayRealloc(oldSources, numOld + numNew);
+        for (long i = 0; i < numNew; i++) {
+            psArrayAdd(oldSources, 1, newSources->data[i]);
+        }
+        psFree(list->tree);
+
+        psVector *x = NULL, *y = NULL;      // Source coordinates
+        stackSourcesParse(&list->bounds, &x, &y, &list->indices, list->sources);
+        list->tree = psTreePlant(2, SOURCES_MAX_LEAF, x, y); // kd Tree with sources
+        psFree(x);
+        psFree(y);
+    }
+
+    if (newDups) {
+        psArray *oldDups = list->duplicates; // Old list of duplicates
+        long numOld = oldDups ? oldDups->n : 0; // Number of old duplicates
+        long numNew = newDups->n;       // Number of new duplicates
+
+        list->duplicates = oldDups = psArrayRealloc(oldDups, numOld + numNew);
+        for (long i = 0; i < numNew; i++) {
+            psArrayAdd(oldDups, 1, newDups->data[i]);
+        }
+    }
 
     return list;
@@ -201,4 +217,5 @@
     psVector *coords = psVectorAlloc(2, PS_TYPE_F32); // Coordinates of source
     psArray *outside = psArrayAllocEmpty(numSources); // Sources that don't correlate
+    psArray *inside = psArrayAllocEmpty(numSources); // Sources that do correlate
     for (long i = 0; i < numSources; i++) {
         coords->data.F32[0] = x->data.F32[i];
@@ -207,7 +224,5 @@
         if (match < 0) {
             numOut++;
-            if (outside) {
-                psArrayAdd(outside, 1, sources->data[indices->data.U32[i]]);
-            }
+            psArrayAdd(outside, 1, sources->data[indices->data.U32[i]]);
             continue;
         }
@@ -220,4 +235,5 @@
             numIn++;
             magDiff->data.F32[numIn] = listSource->psfMag - source->psfMag;
+            psArrayAdd(inside, 1, source);
         }
     }
@@ -256,9 +272,13 @@
                 source->psfMag -= meanDiff;
             }
+            for (long j = 0; j < list->duplicates->n; j++) {
+                pmSource *source = list->duplicates->data[j];
+                source->psfMag -= meanDiff;
+            }
 
             // Suck sources from this list into the first one we found.
-            psTrace("ppStack.sources", 4, "Bridge found: Merging lists.");
-
-            ppStackSourceListExtend(*merge, list->sources);
+            psTrace("ppStack.sources", 4, "Bridge: Merging lists.");
+
+            ppStackSourceListExtend(*merge, list->sources, NULL);
             psFree(list);
             lists->data[listIndex] = NULL;
@@ -269,7 +289,11 @@
                 source->psfMag += meanDiff;
             }
+            for (long j = 0; j < numIn; j++) {
+                pmSource *source = inside->data[j]; // New source
+                source->psfMag += meanDiff;
+            }
             // Put the sources that didn't correlate into the list
-            psTrace("ppStack.sources", 4, "Extending list");
-            ppStackSourceListExtend(list, outside);
+            psTrace("ppStack.sources", 4, "Overlap: Extending list");
+            ppStackSourceListExtend(list, outside, inside);
             *merge = list;
         }
@@ -281,4 +305,5 @@
         psFree(outside);
     }
+    psFree(inside);
 
     return numIn;
@@ -286,14 +311,8 @@
 
 
-psArray *ppStackSourceListAdd(psArray *lists, const pmReadout *inRO, const pmConfig *config)
-{
-    PS_ASSERT_PTR_NON_NULL(inRO, NULL);
+psArray *ppStackSourceListAdd(psArray *lists, psArray *sources, const pmConfig *config)
+{
+    PS_ASSERT_PTR_NON_NULL(sources, NULL);
     PS_ASSERT_PTR_NON_NULL(config, NULL);
-
-    psArray *sources = psMetadataLookupPtr(NULL, inRO->analysis, "PSPHOT.SOURCES");
-    if (!sources) {
-        psError(PS_ERR_UNEXPECTED_NULL, false, "Unable to find sources in readout.");
-        return NULL;
-    }
 
     if (!lists) {
@@ -399,5 +418,5 @@
                 // It doesn't match anything at all.  Merge it in to the first list.
                 psTrace("ppStack.sources", 4, "Disjoint list: Merging into first");
-                ppStackSourceListExtend(firstList, list->sources);
+                ppStackSourceListExtend(firstList, list->sources, NULL);
             }
         }