Index: trunk/src/rtree.c
===================================================================
--- trunk/src/rtree.c	(revision 13906)
+++ trunk/src/rtree.c	(revision 13907)
@@ -373,8 +373,6 @@
 		for (i = 0; i < M_SIZE; i++) {
 			if (!node->u.rects[i].bptr)
 				break;
-			if (node->flags.manage & flag)
-				free((void *) node->u.rects[i].bptr);
 			flag = flag << 1;
 		}
 	else
@@ -387,14 +385,39 @@
 }
 
 /* free the memory associated with an rtree. */
-void pcb_r_destroy_tree(pcb_rtree_t ** rtree)
+void pcb_r_destroy_tree(pcb_rtree_t **rtree)
 {
-
 	__r_destroy_tree((*rtree)->root);
 	free(*rtree);
 	*rtree = NULL;
 }
 
+static void pcb_r_free_tree_data_(struct rtree_node *node, void (*free)(void *ptr))
+{
+	int i;
+
+	if (node->flags.is_leaf) {
+		for (i = 0; i < M_SIZE; i++) {
+			if (!node->u.rects[i].bptr)
+				break;
+			free((void *) node->u.rects[i].bptr);
+			node->u.rects[i].bptr = NULL;
+		}
+	}
+	else {
+		for (i = 0; i < M_SIZE; i++) {
+			if (!node->u.kids[i])
+				break;
+			pcb_r_free_tree_data_(node->u.kids[i], free);
+		}
+	}
+}
+
+void pcb_r_free_tree_data(pcb_rtree_t *rtree, void (*free)(void *ptr))
+{
+	pcb_r_free_tree_data_(rtree->root, free);
+}
+
 typedef struct {
 	pcb_r_dir_t (*check_it) (const pcb_box_t * region, void *cl);
 	pcb_r_dir_t (*found_it) (const pcb_box_t * box, void *cl);
@@ -898,7 +921,7 @@
 	rtree->size++;
 }
 
-pcb_bool __r_delete(struct rtree_node *node, const pcb_box_t * query)
+pcb_bool __r_delete_free_data(struct rtree_node *node, const pcb_box_t * query, void (*free_data)(void *data))
 {
 	int i, flag, mask, a;
 
@@ -925,7 +948,7 @@
 							node->u.rects[i].bptr = NULL;
 						return pcb_true;
 					}
-					return (__r_delete(node->parent, &node->box));
+					return __r_delete_free_data(node->parent, &node->box, free_data);
 				}
 				else
 					/* propagate boundary adjust upward */
@@ -936,7 +959,7 @@
 				return pcb_true;
 			}
 			if (node->u.kids[i]) {
-				if (__r_delete(node->u.kids[i], query))
+				if (__r_delete_free_data(node->u.kids[i], query, free_data))
 					return pcb_true;
 			}
 			else
@@ -961,8 +984,8 @@
 	}
 	if (!node->u.rects[i].bptr)
 		return pcb_false;								/* not at this leaf */
-	if (node->flags.manage & a) {
-		free((void *) node->u.rects[i].bptr);
+	if (free_data != NULL) {
+		free_data((void *) node->u.rects[i].bptr);
 		node->u.rects[i].bptr = NULL;
 	}
 	/* squeeze the manage flags together */
@@ -977,7 +1000,7 @@
 	}
 	if (!node->u.rects[0].bptr) {
 		if (node->parent)
-			__r_delete(node->parent, &node->box);
+			__r_delete_free_data(node->parent, &node->box, free_data);
 		return pcb_true;
 	}
 	else
@@ -989,13 +1012,18 @@
 	return pcb_true;
 }
 
-pcb_bool pcb_r_delete_entry(pcb_rtree_t * rtree, const pcb_box_t * box)
+pcb_bool __r_delete(struct rtree_node *node, const pcb_box_t * query)
 {
+	return __r_delete_free_data(node, query, NULL);
+}
+
+pcb_bool pcb_r_delete_entry_free_data(pcb_rtree_t * rtree, const pcb_box_t * box, void (*free_data)(void *d))
+{
 	pcb_bool r;
 
 	assert(box);
 	assert(rtree);
-	r = __r_delete(rtree->root, box);
+	r = __r_delete_free_data(rtree->root, box, free_data);
 	if (r)
 		rtree->size--;
 #ifdef SLOW_ASSERTS
@@ -1004,7 +1032,12 @@
 	return r;
 }
 
+pcb_bool pcb_r_delete_entry(pcb_rtree_t * rtree, const pcb_box_t * box)
+{
+	return pcb_r_delete_entry_free_data(rtree, box, NULL);
+}
 
+
 static pcb_box_t *pcb_r_next_(pcb_rtree_it_t *it, struct rtree_node *curr)
 {
 	int n;
Index: trunk/src/rtree.h
===================================================================
--- trunk/src/rtree.h	(revision 13906)
+++ trunk/src/rtree.h	(revision 13907)
@@ -70,8 +70,15 @@
 void pcb_r_create_insert_array(pcb_rtree_t *rtree, const pcb_box_t *boxlist[], int N, int manage);
 
 pcb_bool pcb_r_delete_entry(pcb_rtree_t * rtree, const pcb_box_t * which);
+
+/* also free leaf data using free_data() */
+pcb_bool __r_delete_free_data(struct rtree_node *node, const pcb_box_t * query, void (*free_data)(void *data));
+pcb_bool pcb_r_delete_entry_free_data(pcb_rtree_t * rtree, const pcb_box_t * box, void (*free_data)(void *d));
+
+
 void pcb_r_insert_entry(pcb_rtree_t * rtree, const pcb_box_t * which, int manage);
 
+
 /* generic search routine */
 /* region_in_search should return pcb_true if "what you're looking for" is
  * within the specified region; regions, like rectangles, are closed on
@@ -111,5 +118,7 @@
 /* Free fields of the iterator */
 void pcb_r_end(pcb_rtree_it_t *it);
 
+/* Recursively call free() on all leaf data */
+void pcb_r_free_tree_data(pcb_rtree_t *rtree, void (*free)(void *ptr));
 
 #endif
Index: trunk/src_plugins/autoplace/autoplace.c
===================================================================
--- trunk/src_plugins/autoplace/autoplace.c	(revision 13906)
+++ trunk/src_plugins/autoplace/autoplace.c	(revision 13907)
@@ -610,9 +610,9 @@
 		PCB_END_LOOP;
 
 		rt_s = pcb_r_create_tree();
-		pcb_r_create_insert_array(rt_s, (const pcb_box_t **) seboxes.array, vtp0_len(&seboxes), 1);
+		pcb_r_create_insert_array(rt_s, (const pcb_box_t **) seboxes.array, vtp0_len(&seboxes), 0);
 		rt_c = pcb_r_create_tree();
-		pcb_r_create_insert_array(rt_c, (const pcb_box_t **) ceboxes.array, vtp0_len(&ceboxes), 1);
+		pcb_r_create_insert_array(rt_c, (const pcb_box_t **) ceboxes.array, vtp0_len(&ceboxes), 0);
 		vtp0_uninit(&seboxes);
 		vtp0_uninit(&ceboxes);
 		/* now, for each element, find its neighbor on all four sides */
@@ -676,6 +676,8 @@
 			PCB_END_LOOP;
 		}
 		/* free k-d tree memory */
+		pcb_r_free_tree_data(rt_s, free);
+		pcb_r_free_tree_data(rt_c, free);
 		pcb_r_destroy_tree(&rt_s);
 		pcb_r_destroy_tree(&rt_c);
 	}
Index: trunk/src_plugins/autoroute/autoroute.c
===================================================================
--- trunk/src_plugins/autoroute/autoroute.c	(revision 13906)
+++ trunk/src_plugins/autoroute/autoroute.c	(revision 13907)
@@ -1277,7 +1277,7 @@
 	for (i = 0; i < pcb_max_group(PCB); i++) {
 		/* create the r-tree */
 		rd->layergrouptree[i] = pcb_r_create_tree();
-		pcb_r_create_insert_array(rd->layergrouptree[i], (const pcb_box_t **) layergroupboxes[i].array, vtp0_len(&layergroupboxes[i]), 1);
+		pcb_r_create_insert_array(rd->layergrouptree[i], (const pcb_box_t **) layergroupboxes[i].array, vtp0_len(&layergroupboxes[i]), 0);
 	}
 
 	if (AutoRouteParameters.use_vias) {
@@ -1305,8 +1305,10 @@
 void DestroyRouteData(routedata_t ** rd)
 {
 	int i;
-	for (i = 0; i < pcb_max_group(PCB); i++)
+	for (i = 0; i < pcb_max_group(PCB); i++) {
+		pcb_r_free_tree_data((*rd)->layergrouptree[i], free);
 		pcb_r_destroy_tree(&(*rd)->layergrouptree[i]);
+	}
 	if (AutoRouteParameters.use_vias)
 		mtspace_destroy(&(*rd)->mtspace);
 /*	free((*rd)->layergrouptree);*/
@@ -3002,7 +3004,7 @@
 	MergeNets(rb, subnet, NET);
 	MergeNets(rb, subnet, SUBNET);
 	/* add it to the r-tree, this may be the whole route! */
-	pcb_r_insert_entry(rd->layergrouptree[rb->group], &rb->box, 1);
+	pcb_r_insert_entry(rd->layergrouptree[rb->group], &rb->box, 0);
 	rb->flags.homeless = 0;
 }
 
@@ -3054,7 +3056,7 @@
 		MergeNets(rb, subnet, SUBNET);
 		assert(__routepcb_box_is_good(rb));
 		/* and add it to the r-tree! */
-		pcb_r_insert_entry(rd->layergrouptree[rb->group], &rb->box, 1);
+		pcb_r_insert_entry(rd->layergrouptree[rb->group], &rb->box, 0);
 		rb->flags.homeless = 0;			/* not homeless anymore */
 		rb->livedraw_obj.via = live_via;
 	}
@@ -3138,7 +3140,7 @@
 	MergeNets(rb, qsn, SUBNET);
 	assert(__routepcb_box_is_good(rb));
 	/* and add it to the r-tree! */
-	pcb_r_insert_entry(rd->layergrouptree[rb->group], &rb->box, 1);
+	pcb_r_insert_entry(rd->layergrouptree[rb->group], &rb->box, 0);
 
 	if (conf_core.editor.live_routing) {
 		pcb_layer_t *layer = LAYER_PTR(PCB->LayerGroups.grp[rb->group].lid[0]);
@@ -3951,7 +3953,7 @@
 				/*assert (!pcb_r_search(rd->layergrouptree[e->rb->group],
 				   &e->rb->box, NULL, no_planes,0));
 				 */
-				pcb_r_insert_entry(rd->layergrouptree[e->rb->group], &e->rb->box, 1);
+				pcb_r_insert_entry(rd->layergrouptree[e->rb->group], &e->rb->box, 0);
 				e->rb->flags.homeless = 0;	/* not homeless any more */
 				/* add to vector of all expansion areas in r-tree */
 				vector_append(area_vec, e->rb);
@@ -4088,7 +4090,7 @@
 			if (!pcb_box_is_good(&ans->inflated))
 				goto dontexpand;
 			nrb = CreateExpansionArea(&ans->inflated, e->rb->group, e->rb, pcb_true, e);
-			pcb_r_insert_entry(rd->layergrouptree[nrb->group], &nrb->box, 1);
+			pcb_r_insert_entry(rd->layergrouptree[nrb->group], &nrb->box, 0);
 			vector_append(area_vec, nrb);
 			nrb->flags.homeless = 0;	/* not homeless any more */
 			broken = BreakManyEdges(&s, targets, rd->layergrouptree[nrb->group], area_vec, ans, nrb, e);
@@ -4161,7 +4163,7 @@
 		assert(!rb->flags.homeless);
 		if (rb->conflicts_with && rb->parent.expansion_area->conflicts_with != rb->conflicts_with)
 			vector_destroy(&rb->conflicts_with);
-		pcb_r_delete_entry(rd->layergrouptree[rb->group], &rb->box);
+		pcb_r_delete_entry_free_data(rd->layergrouptree[rb->group], &rb->box, free);
 	}
 	vector_destroy(&area_vec);
 	/* clean up; remove all 'source', 'target', and 'nobloat' flags */
@@ -4377,7 +4379,7 @@
 #ifndef NDEBUG
 						del =
 #endif
-							pcb_r_delete_entry(rd->layergrouptree[p->group], &p->box);
+							pcb_r_delete_entry_free_data(rd->layergrouptree[p->group], &p->box, free);
 #ifndef NDEBUG
 						assert(del);
 #endif