Index: trunk/src/action_helper.c
===================================================================
--- trunk/src/action_helper.c	(revision 11679)
+++ trunk/src/action_helper.c	(revision 11680)
@@ -952,7 +952,9 @@
 																									 pcb_crosshair.AttachedBox.Point1.X,
 																									 pcb_crosshair.AttachedBox.Point1.Y,
 																									 pcb_crosshair.AttachedBox.Point2.X,
-																									 pcb_crosshair.AttachedBox.Point2.Y, pcb_flag_make(flags))) != NULL) {
+																									 pcb_crosshair.AttachedBox.Point2.Y,
+																									 2 * conf_core.design.clearance,
+																									 pcb_flag_make(flags))) != NULL) {
 				pcb_obj_add_attribs(polygon, PCB->pen_attr);
 				pcb_undo_add_obj_to_create(PCB_TYPE_POLYGON, CURRENT, polygon, polygon);
 				pcb_undo_inc_serial();
Index: trunk/src/obj_poly.c
===================================================================
--- trunk/src/obj_poly.c	(revision 11679)
+++ trunk/src/obj_poly.c	(revision 11680)
@@ -194,9 +194,9 @@
 }
 
 /* creates a new polygon from the old formats rectangle data */
-pcb_polygon_t *pcb_poly_new_from_rectangle(pcb_layer_t *Layer, pcb_coord_t X1, pcb_coord_t Y1, pcb_coord_t X2, pcb_coord_t Y2, pcb_flag_t Flags)
+pcb_polygon_t *pcb_poly_new_from_rectangle(pcb_layer_t *Layer, pcb_coord_t X1, pcb_coord_t Y1, pcb_coord_t X2, pcb_coord_t Y2, pcb_coord_t Clearance, pcb_flag_t Flags)
 {
-	pcb_polygon_t *polygon = pcb_poly_new(Layer, Flags);
+	pcb_polygon_t *polygon = pcb_poly_new(Layer, Clearance, Flags);
 	if (!polygon)
 		return (polygon);
 
@@ -219,7 +219,7 @@
 }
 
 /* creates a new polygon on a layer */
-pcb_polygon_t *pcb_poly_new(pcb_layer_t *Layer, pcb_flag_t Flags)
+pcb_polygon_t *pcb_poly_new(pcb_layer_t *Layer, pcb_coord_t Clearance, pcb_flag_t Flags)
 {
 	pcb_polygon_t *polygon = pcb_poly_alloc(Layer);
 
@@ -226,6 +226,7 @@
 	/* copy values */
 	polygon->Flags = Flags;
 	polygon->ID = pcb_create_ID_get();
+	polygon->Clearance = Clearance;
 	polygon->Clipped = NULL;
 	polygon->NoHoles = NULL;
 	polygon->NoHolesValid = 0;
@@ -243,7 +244,7 @@
 pcb_polygon_t *pcb_poly_dup(pcb_layer_t *dst, pcb_polygon_t *src)
 {
 	pcb_board_t *pcb;
-	pcb_polygon_t *p = pcb_poly_new(dst, src->Flags);
+	pcb_polygon_t *p = pcb_poly_new(dst, src->Clearance, src->Flags);
 	pcb_poly_copy(p, src, 0, 0);
 	pcb_add_polygon_on_layer(dst, p);
 	pcb_poly_copy_meta(p, src);
@@ -257,7 +258,7 @@
 pcb_polygon_t *pcb_poly_dup_at(pcb_layer_t *dst, pcb_polygon_t *src, pcb_coord_t dx, pcb_coord_t dy)
 {
 	pcb_board_t *pcb;
-	pcb_polygon_t *p = pcb_poly_new(dst, src->Flags);
+	pcb_polygon_t *p = pcb_poly_new(dst, src->Clearance, src->Flags);
 	pcb_poly_copy(p, src, dx, dy);
 	pcb_add_polygon_on_layer(dst, p);
 	pcb_poly_copy_meta(p, src);
@@ -350,7 +351,7 @@
 	pcb_layer_t *layer = &ctx->buffer.dst->Layer[pcb_layer_id(ctx->buffer.src, Layer)];
 	pcb_polygon_t *polygon;
 
-	polygon = pcb_poly_new(layer, Polygon->Flags);
+	polygon = pcb_poly_new(layer, Polygon->Clearance, Polygon->Flags);
 	pcb_poly_copy(polygon, Polygon, 0, 0);
 	pcb_poly_copy_meta(polygon, Polygon);
 
@@ -766,7 +767,7 @@
 {
 	pcb_polygon_t *polygon;
 
-	polygon = pcb_poly_new(Layer, pcb_no_flags());
+	polygon = pcb_poly_new(Layer, Polygon->Clearance, pcb_no_flags());
 	pcb_poly_copy(polygon, Polygon, ctx->copy.DeltaX, ctx->copy.DeltaY);
 	pcb_poly_copy_meta(polygon, Polygon);
 	if (!Layer->polygon_tree)
Index: trunk/src/obj_poly.h
===================================================================
--- trunk/src/obj_poly.h	(revision 11679)
+++ trunk/src/obj_poly.h	(revision 11680)
@@ -56,8 +56,8 @@
 void pcb_poly_free_fields(pcb_polygon_t * polygon);
 
 void pcb_poly_bbox(pcb_polygon_t *Polygon);
-pcb_polygon_t *pcb_poly_new_from_rectangle(pcb_layer_t *Layer, pcb_coord_t X1, pcb_coord_t Y1, pcb_coord_t X2, pcb_coord_t Y2, pcb_flag_t Flags);
-pcb_polygon_t *pcb_poly_new(pcb_layer_t *Layer, pcb_flag_t Flags);
+pcb_polygon_t *pcb_poly_new_from_rectangle(pcb_layer_t *Layer, pcb_coord_t X1, pcb_coord_t Y1, pcb_coord_t X2, pcb_coord_t Y2, pcb_coord_t Clearance, pcb_flag_t Flags);
+pcb_polygon_t *pcb_poly_new(pcb_layer_t *Layer, pcb_coord_t Clearance, pcb_flag_t Flags);
 pcb_polygon_t *pcb_poly_dup(pcb_layer_t *dst, pcb_polygon_t *src);
 pcb_polygon_t *pcb_poly_dup_at(pcb_layer_t *dst, pcb_polygon_t *src, pcb_coord_t dx, pcb_coord_t dy);
 pcb_point_t *pcb_poly_point_new(pcb_polygon_t *Polygon, pcb_coord_t X, pcb_coord_t Y);
Index: trunk/src/obj_subc.c
===================================================================
--- trunk/src/obj_subc.c	(revision 11679)
+++ trunk/src/obj_subc.c	(revision 11680)
@@ -202,7 +202,7 @@
 
 				pcb_sqline_to_rect(line, x, y);
 
-				poly = pcb_poly_new(dst, pcb_no_flags());
+				poly = pcb_poly_new(dst, line->Clearance, pcb_no_flags());
 				for(n = 0; n < 4; n++)
 					pcb_poly_point_new(poly, x[n], y[n]);
 				pcb_add_polygon_on_layer(dst, poly);
Index: trunk/src/polygon.c
===================================================================
--- trunk/src/polygon.c	(revision 11679)
+++ trunk/src/polygon.c	(revision 11680)
@@ -1515,7 +1515,7 @@
 	int saveID;
 
 	/* move data to layer and clear attached struct */
-	polygon = pcb_poly_new(CURRENT, pcb_no_flags());
+	polygon = pcb_poly_new(CURRENT, 2 * conf_core.design.clearance, pcb_no_flags());
 	saveID = polygon->ID;
 	poly_copy_data(polygon, &pcb_crosshair.AttachedPolygon);
 	polygon->ID = saveID;
@@ -2004,7 +2004,7 @@
 		pcb_polygon_t *newone;
 
 		if (p->contours->area > PCB->IsleArea) {
-			newone = pcb_poly_new(layer, flags);
+			newone = pcb_poly_new(layer, poly->Clearance, flags);
 			if (!newone)
 				return pcb_false;
 			many = pcb_true;
@@ -2098,7 +2098,7 @@
 
 	pa = Input;
 	do {
-		Polygon = pcb_poly_new(Layer, Flags);
+		Polygon = pcb_poly_new(Layer, 2 * conf_core.design.clearance, Flags);
 
 		pline = pa->contours;
 		outer = pcb_true;
Index: trunk/src_plugins/fontmode/fontmode.c
===================================================================
--- trunk/src_plugins/fontmode/fontmode.c	(revision 11679)
+++ trunk/src_plugins/fontmode/fontmode.c	(revision 11680)
@@ -84,7 +84,7 @@
 	pcb_polygon_t *np;
 	
 	/* alloc */
-	np = pcb_poly_new(layer, pcb_no_flags());
+	np = pcb_poly_new(layer, 0, pcb_no_flags());
 	pcb_poly_copy(np, poly, ox, oy);
 
 	/* add */
Index: trunk/src_plugins/io_autotrax/read.c
===================================================================
--- trunk/src_plugins/io_autotrax/read.c	(revision 11679)
+++ trunk/src_plugins/io_autotrax/read.c	(revision 11680)
@@ -690,7 +690,7 @@
 	}
 
 	if (PCB_layer >= 0 && el == NULL) {
-		polygon = pcb_poly_new(&st->pcb->Data->Layer[PCB_layer], flags);
+		polygon = pcb_poly_new(&st->pcb->Data->Layer[PCB_layer], 0, flags);
 	} else if (PCB_layer < 0 && el == NULL){
 		pcb_message(PCB_MSG_ERROR, "Invalid free fill layer found, %s:%d\n", st->Filename, st->lineno);
 	}
Index: trunk/src_plugins/io_eagle/read.c
===================================================================
--- trunk/src_plugins/io_eagle/read.c	(revision 11679)
+++ trunk/src_plugins/io_eagle/read.c	(revision 11680)
@@ -1062,7 +1062,7 @@
 		return 0;
 	}
 
-	poly = pcb_poly_new(&st->pcb->Data->Layer[ly->ly], pcb_flag_make(PCB_FLAG_CLEARPOLY));
+	poly = pcb_poly_new(&st->pcb->Data->Layer[ly->ly], 0, pcb_flag_make(PCB_FLAG_CLEARPOLY));
 
 	for(n = CHILDREN(subtree); n != NULL; n = NEXT(n)) {
 		if (STRCMP(NODENAME(n), "vertex") == 0) {
Index: trunk/src_plugins/io_kicad/read.c
===================================================================
--- trunk/src_plugins/io_kicad/read.c	(revision 11679)
+++ trunk/src_plugins/io_kicad/read.c	(revision 11680)
@@ -2144,7 +2144,7 @@
 					if (PCBLayer < 0) {
 						return kicad_warning(subtree, "parse error: zone layer <0.");
 					}
-					polygon = pcb_poly_new(&st->PCB->Data->Layer[PCBLayer], flags);
+					polygon = pcb_poly_new(&st->PCB->Data->Layer[PCBLayer], 0, flags);
 				} else {
 					return kicad_error(subtree, "unexpected zone layer null node.");
 				}
Index: trunk/src_plugins/io_pcb/parse_y.c
===================================================================
--- trunk/src_plugins/io_pcb/parse_y.c	(revision 11679)
+++ trunk/src_plugins/io_pcb/parse_y.c	(revision 11680)
@@ -2256,7 +2256,7 @@
 #line 927 "parse_y.y" /* yacc.c:1646  */
     {
 				pcb_poly_new_from_rectangle(Layer,
-					OU ((yyvsp[-5].measure)), OU ((yyvsp[-4].measure)), OU ((yyvsp[-5].measure)) + OU ((yyvsp[-3].measure)), OU ((yyvsp[-4].measure)) + OU ((yyvsp[-2].measure)), pcb_flag_old((yyvsp[-1].integer)));
+					OU ((yyvsp[-5].measure)), OU ((yyvsp[-4].measure)), OU ((yyvsp[-5].measure)) + OU ((yyvsp[-3].measure)), OU ((yyvsp[-4].measure)) + OU ((yyvsp[-2].measure)), 0, pcb_flag_old((yyvsp[-1].integer)));
 			}
 #line 2262 "parse_y.c" /* yacc.c:1646  */
     break;
@@ -2379,7 +2379,7 @@
   case 101:
 #line 1164 "parse_y.y" /* yacc.c:1646  */
     {
-				Polygon = pcb_poly_new(Layer, (yyvsp[-2].flagtype));
+				Polygon = pcb_poly_new(Layer, 0, (yyvsp[-2].flagtype));
 			}
 #line 2385 "parse_y.c" /* yacc.c:1646  */
     break;
Index: trunk/src_plugins/io_pcb/parse_y.y
===================================================================
--- trunk/src_plugins/io_pcb/parse_y.y	(revision 11679)
+++ trunk/src_plugins/io_pcb/parse_y.y	(revision 11680)
@@ -926,7 +926,7 @@
 		| T_RECTANGLE '(' measure measure measure measure INTEGER ')'
 			{
 				pcb_poly_new_from_rectangle(Layer,
-					OU ($3), OU ($4), OU ($3) + OU ($5), OU ($4) + OU ($6), pcb_flag_old($7));
+					OU ($3), OU ($4), OU ($3) + OU ($5), OU ($4) + OU ($6), 0, pcb_flag_old($7));
 			}
 		| text_hi_format
 		| text_newformat
@@ -1162,7 +1162,7 @@
 		: /* flags are passed in */
 		T_POLYGON '(' flags ')' '('
 			{
-				Polygon = pcb_poly_new(Layer, $3);
+				Polygon = pcb_poly_new(Layer, 0, $3);
 			}
 		  polygonpoints
 		  polygonholes ')'
Index: trunk/src_plugins/lib_gtk_common/dlg_propedit.c
===================================================================
--- trunk/src_plugins/lib_gtk_common/dlg_propedit.c	(revision 11679)
+++ trunk/src_plugins/lib_gtk_common/dlg_propedit.c	(revision 11680)
@@ -347,7 +347,7 @@
 	v = pcb_poly_new_from_rectangle(preview_pcb.Data->Layer + 0,
 																									 PCB_MIL_TO_COORD(10), PCB_MIL_TO_COORD(10),
 																									 PCB_MIL_TO_COORD(1200), PCB_MIL_TO_COORD(1200),
-																									 pcb_flag_make(PCB_FLAG_CLEARPOLY));
+																									 0, pcb_flag_make(PCB_FLAG_CLEARPOLY));
 	pcb_poly_init_clip(preview_pcb.Data, preview_pcb.Data->Layer + 0, v);
 	PCB = old_pcb;
 
Index: trunk/src_plugins/millpath/toolpath.c
===================================================================
--- trunk/src_plugins/millpath/toolpath.c	(revision 11679)
+++ trunk/src_plugins/millpath/toolpath.c	(revision 11680)
@@ -179,10 +179,10 @@
 				pcb_box_bump_box(&otlbb, (pcb_box_t *)arc);
 			pcb_r_end(&it);
 		}
-		result->fill = pcb_poly_new_from_rectangle(result->res_ply, otlbb.X1, otlbb.Y1, otlbb.X2, otlbb.Y2, pcb_flag_make(PCB_FLAG_FULLPOLY));
+		result->fill = pcb_poly_new_from_rectangle(result->res_ply, otlbb.X1, otlbb.Y1, otlbb.X2, otlbb.Y2, 0, pcb_flag_make(PCB_FLAG_FULLPOLY));
 	}
 	else
-		result->fill = pcb_poly_new_from_rectangle(result->res_ply, 0, 0, pcb->MaxWidth, pcb->MaxHeight, pcb_flag_make(PCB_FLAG_FULLPOLY));
+		result->fill = pcb_poly_new_from_rectangle(result->res_ply, 0, 0, pcb->MaxWidth, pcb->MaxHeight, 0, pcb_flag_make(PCB_FLAG_FULLPOLY));
 
 	pcb_poly_init_clip(pcb->Data, result->res_ply, result->fill);