fix(core): report overlapping pairs through PartOverlapChecker

The console overlap check and the MCP check_overlaps tool counted
crossing points, so a part contained in or stacked on another reported
no overlap. Both now list pairs from PartOverlapChecker.FindOverlappingPairs,
which uses the Intersects verdict and skips cut-off parts.

Plate.HasOverlappingParts stays for now: two test files outside this
change still call it.

Co-Authored-By: Claude Fable 5.2 <noreply@anthropic.com>

OpenNest.Console/Program.cs

@@ -789,14 +789,14 @@ static class NestConsole
         var total = 0;
         foreach (var plate in plates.Where(p => p.Parts.Count > 0))
         {
-            var hasOverlaps = plate.HasOverlappingParts(out var overlapPts);
+            var overlapping = PartOverlapChecker.FindOverlappingPairs(plate.Parts);
             var label = plates.Count > 1 ? $"Plate {nest.Plates.IndexOf(plate)}: " : "";
             Console.WriteLine(
-                hasOverlaps
-                    ? $"{label}OVERLAPS DETECTED: {overlapPts.Count} intersection points"
+                overlapping.Count > 0
+                    ? $"{label}OVERLAPS DETECTED: {overlapping.Count} overlapping pair(s)"
                     : $"{label}Overlap check: PASS"
             );
-            total += overlapPts.Count;
+            total += overlapping.Count;
         }
 
         return total;

OpenNest.Core/PartOverlapChecker.cs

@@ -57,6 +57,54 @@ namespace OpenNest
             );
         }
 
+        /// <summary>
+        /// Every overlapping pair among <paramref name="parts"/>, in list order (First precedes
+        /// Second). Cut-off parts are skipped. Each verdict is <see cref="Overlaps"/>, so a part
+        /// contained in or stacked on another is reported even though their outlines never cross.
+        /// </summary>
+        public static List<(Part First, Part Second)> FindOverlappingPairs(IEnumerable<Part> parts)
+        {
+            var pairs = new List<(Part First, Part Second)>();
+            var realParts = new List<Part>();
+
+            foreach (var part in parts)
+            {
+                if (!part.BaseDrawing.IsCutOff)
+                    realParts.Add(part);
+            }
+
+            var checker = new PartOverlapChecker();
+
+            for (var i = 0; i < realParts.Count; i++)
+            {
+                var part1 = realParts[i];
+                var b1 = part1.BoundingBox;
+
+                for (var j = i + 1; j < realParts.Count; j++)
+                {
+                    var part2 = realParts[j];
+                    var b2 = part2.BoundingBox;
+
+                    // Skip pairs whose bounding boxes don't meaningfully overlap.
+                    // Floating-point rounding can produce sub-epsilon overlaps for
+                    // parts that are merely edge-touching, so require the overlap
+                    // region to exceed Epsilon in both dimensions.
+                    var overlapX =
+                        System.Math.Min(b1.Right, b2.Right) - System.Math.Max(b1.Left, b2.Left);
+                    var overlapY =
+                        System.Math.Min(b1.Top, b2.Top) - System.Math.Max(b1.Bottom, b2.Bottom);
+
+                    if (overlapX <= Math.Tolerance.Epsilon || overlapY <= Math.Tolerance.Epsilon)
+                        continue;
+
+                    if (checker.Overlaps(part1, part2))
+                        pairs.Add((part1, part2));
+                }
+            }
+
+            return pairs;
+        }
+
         private PreparedProgram Prepare(CNC.Program program)
         {
             if (!programs.TryGetValue(program, out var prepared))

OpenNest.Mcp/Tools/InspectionTools.cs

@@ -109,7 +109,7 @@ namespace OpenNest.Mcp.Tools
         }
 
         [McpServerTool(Name = "check_overlaps")]
-        [Description("Check a plate for overlapping parts. Reports collision points if any.")]
+        [Description("Check a plate for overlapping parts. Reports the overlapping pairs by part index if any.")]
         public string CheckOverlaps([Description("Index of the plate")] int plateIndex)
         {
             var plate = _session.GetPlate(plateIndex);
@@ -119,24 +119,26 @@ namespace OpenNest.Mcp.Tools
             if (plate.Parts.Count < 2)
                 return $"Plate {plateIndex}: no overlaps possible (fewer than 2 parts)";
 
-            var hasOverlaps = plate.HasOverlappingParts(out var pts);
+            var pairs = PartOverlapChecker.FindOverlappingPairs(plate.Parts);
 
-            if (!hasOverlaps)
+            if (pairs.Count == 0)
                 return $"Plate {plateIndex}: no overlapping parts detected";
 
             var sb = new StringBuilder();
-            sb.AppendLine($"Plate {plateIndex}: {pts.Count} collision point(s) detected!");
+            sb.AppendLine($"Plate {plateIndex}: {pairs.Count} overlapping pair(s) detected!");
 
-            var limit = System.Math.Min(pts.Count, 20);
+            var limit = System.Math.Min(pairs.Count, 20);
 
             for (var i = 0; i < limit; i++)
             {
-                var pt = pts[i];
-                sb.AppendLine($"  Collision at ({pt.X:F2}, {pt.Y:F2})");
+                var (first, second) = pairs[i];
+                sb.AppendLine(
+                    $"  Part {plate.Parts.IndexOf(first)} overlaps part {plate.Parts.IndexOf(second)}"
+                );
             }
 
-            if (pts.Count > limit)
-                sb.AppendLine($"  ... and {pts.Count - limit} more collision points");
+            if (pairs.Count > limit)
+                sb.AppendLine($"  ... and {pairs.Count - limit} more overlapping pairs");
 
             return sb.ToString();
         }

OpenNest.Tests/CommonLines/CommonLinePlanningTests.cs

@@ -254,7 +254,7 @@ public class CommonLinePlanningTests
         nest.Drawings.Add(drawing);
         var utilization = plate.Utilization();
         var nested = drawing.Quantity.Nested;
-        var overlaps = plate.HasOverlappingParts(out _);
+        var overlaps = PartOverlapChecker.FindOverlappingPairs(plate.Parts).Count;
         var pairs = PlateOverlapAnalyzer.Analyze(plate.Parts.ToList()).Pairs.Count;
         var area = plate.Parts.Sum(p => p.BaseDrawing.Area);
 
@@ -267,7 +267,7 @@ public class CommonLinePlanningTests
         Assert.All(plate.Parts.Skip(1), p => Assert.True(CommonLineCuts.IsSinglePass(p.Program)));
         Assert.Equal(utilization, plate.Utilization(), 12);
         Assert.Equal(nested, drawing.Quantity.Nested);
-        Assert.Equal(overlaps, plate.HasOverlappingParts(out _));
+        Assert.Equal(overlaps, PartOverlapChecker.FindOverlappingPairs(plate.Parts).Count);
         Assert.Equal(pairs, PlateOverlapAnalyzer.Analyze(plate.Parts.ToList()).Pairs.Count);
         Assert.Equal(area, plate.Parts.Sum(p => p.BaseDrawing.Area), 12);
         Assert.True(CommonLineGeometry.Check(plate.CommonLines[0]).IsIntact);

OpenNest.Tests/CutOffs/CutOffTests.cs

@@ -44,7 +44,7 @@ public class CutOffTests
     }
 
     [Fact]
-    public void Plate_HasOverlappingParts_SkipsCutOffParts()
+    public void FindOverlappingPairs_SkipsCutOffParts()
     {
         var pgm = new Program();
         pgm.Codes.Add(new RapidMove(new Vector(0, 0)));
@@ -60,8 +60,30 @@ public class CutOffTests
         plate.Parts.Add(new Part(realDrawing));
         plate.Parts.Add(new Part(cutoffDrawing));
 
-        var hasOverlap = plate.HasOverlappingParts(out var pts);
-        Assert.False(hasOverlap);
+        Assert.Empty(PartOverlapChecker.FindOverlappingPairs(plate.Parts));
+    }
+
+    [Fact]
+    public void FindOverlappingPairs_ReportsTheSameStackedPartsWhenNeitherIsACutOff()
+    {
+        // Control for the test above: the same two stacked squares overlap, so only the
+        // cut-off flag keeps that pair out of the result.
+        var pgm = new Program();
+        pgm.Codes.Add(new RapidMove(new Vector(0, 0)));
+        pgm.Codes.Add(new LinearMove(new Vector(10, 0)));
+        pgm.Codes.Add(new LinearMove(new Vector(10, 10)));
+        pgm.Codes.Add(new LinearMove(new Vector(0, 10)));
+        pgm.Codes.Add(new LinearMove(new Vector(0, 0)));
+
+        var plate = new Plate(100, 100);
+        var first = new Part(new Drawing("real", pgm));
+        var second = new Part(new Drawing("also real", pgm));
+        plate.Parts.Add(first);
+        plate.Parts.Add(second);
+
+        var pair = Assert.Single(PartOverlapChecker.FindOverlappingPairs(plate.Parts));
+        Assert.Same(first, pair.First);
+        Assert.Same(second, pair.Second);
     }
 
     [Fact]

OpenNest.Tests/Engine/EngineOverlapTests.cs

@@ -62,18 +62,15 @@ public class EngineOverlapTests
         foreach (var g in rotGroups)
             _output.WriteLine($"  Rotation {g.Key:F1}°: {g.Count()} parts");
 
-        var hasOverlaps = plate.HasOverlappingParts(out var collisionPoints);
-        _output.WriteLine($"Overlaps: {hasOverlaps} ({collisionPoints.Count} collision pts)");
+        var pairs = PartOverlapChecker.FindOverlappingPairs(plate.Parts);
+        _output.WriteLine($"Overlaps: {pairs.Count > 0} ({pairs.Count} overlapping pair(s))");
 
-        if (hasOverlaps)
-        {
-            for (var i = 0; i < System.Math.Min(collisionPoints.Count, 10); i++)
-                _output.WriteLine($"  ({collisionPoints[i].X:F2}, {collisionPoints[i].Y:F2})");
-        }
+        foreach (var (first, second) in pairs.Take(10))
+            _output.WriteLine($"  part {plate.Parts.IndexOf(first)} overlaps part {plate.Parts.IndexOf(second)}");
 
-        Assert.False(
-            hasOverlaps,
-            $"Strategy '{strategy}' produced {collisionPoints.Count} collision point(s) with {plate.Parts.Count} parts"
+        Assert.True(
+            pairs.Count == 0,
+            $"Strategy '{strategy}' produced {pairs.Count} overlapping pair(s) with {plate.Parts.Count} parts"
         );
     }
 
@@ -87,11 +84,11 @@ public class EngineOverlapTests
             TestHelpers.MakePartAt(10, 0, 10)
         );
 
-        var hasOverlaps = plate.HasOverlappingParts(out var pts);
-        _output.WriteLine($"Adjacent squares: overlaps={hasOverlaps}, collision count={pts.Count}");
+        var pairs = PartOverlapChecker.FindOverlappingPairs(plate.Parts);
+        _output.WriteLine($"Adjacent squares: overlapping pairs={pairs.Count}");
 
-        Assert.False(
-            hasOverlaps,
+        Assert.True(
+            pairs.Count == 0,
             "Adjacent edge-touching parts should not be reported as overlapping"
         );
     }

OpenNest.Tests/Engine/EngineRefactorSmokeTests.cs

@@ -72,7 +72,7 @@ public class EngineRefactorSmokeTests
 
         Assert.Equal(23, parts.Count);
         plate.Parts.AddRange(parts);
-        Assert.False(plate.HasOverlappingParts(out _), "Fill overlaps");
+        Assert.Empty(PartOverlapChecker.FindOverlappingPairs(plate.Parts));
         var area = plate.WorkArea();
         Assert.All(parts, p => Assert.True(
             p.BoundingBox.Left >= area.Left - 1e-6 && p.BoundingBox.Right <= area.Right + 1e-6

OpenNest.Tests/Fill/FillLinearMaxPartsTests.cs

@@ -79,7 +79,7 @@ public class FillLinearMaxPartsTests
         Assert.Equal(3, parts.Count);
         var plate = new Plate(width, length) { PartSpacing = Spacing };
         plate.Parts.AddRange(parts);
-        Assert.False(plate.HasOverlappingParts(out _));
+        Assert.Empty(PartOverlapChecker.FindOverlappingPairs(plate.Parts));
         Assert.All(parts, part => Assert.True(part.BoundingBox.Right <= area.Right
             && part.BoundingBox.Top <= area.Top));
     }

OpenNest.Tests/Fill/PairRemnantFillerTests.cs

@@ -59,7 +59,7 @@ public class PairRemnantFillerTests
 
         var check = new Plate { Size = new Size(60, 120), PartSpacing = Spacing };
         check.Parts.AddRange(withPairs);
-        Assert.False(check.HasOverlappingParts(out _));
+        Assert.Empty(PartOverlapChecker.FindOverlappingPairs(check.Parts));
     }
 
     [Fact]

OpenNest.Tests/Fill/PartOverlapCheckerTests.cs

@@ -411,6 +411,76 @@ public class PartOverlapCheckerTests
         return pattern;
     }
 
+    [Fact]
+    public void FindOverlappingPairs_ReportsAContainedPart()
+    {
+        // The small square sits wholly inside the large one: no outlines cross, so there
+        // are no crossing points to count, but the material overlaps.
+        var outer = TestHelpers.MakePartAt(0, 0, 10);
+        var inner = TestHelpers.MakePartAt(4, 4, 2);
+
+        Assert.True(outer.Intersects(inner, out var points));
+        Assert.Empty(points);
+
+        var pair = Assert.Single(PartOverlapChecker.FindOverlappingPairs(new[] { outer, inner }));
+        Assert.Same(outer, pair.First);
+        Assert.Same(inner, pair.Second);
+    }
+
+    [Fact]
+    public void FindOverlappingPairs_IgnoresEdgeTouchingParts()
+    {
+        var parts = new[]
+        {
+            TestHelpers.MakePartAt(0, 0, 10),
+            TestHelpers.MakePartAt(10, 0, 10),
+            TestHelpers.MakePartAt(0, 10, 10),
+            TestHelpers.MakePartAt(10, 10, 10),
+        };
+
+        Assert.Empty(PartOverlapChecker.FindOverlappingPairs(parts));
+    }
+
+    [Fact]
+    public void FindOverlappingPairs_ExcludesCutOffParts()
+    {
+        var real = TestHelpers.MakePartAt(0, 0, 10);
+        var other = TestHelpers.MakePartAt(5, 5, 10);
+        var cutOff = TestHelpers.MakePartAt(2, 2, 10);
+        cutOff.BaseDrawing.IsCutOff = true;
+
+        var pair = Assert.Single(PartOverlapChecker.FindOverlappingPairs(new[] { real, cutOff, other }));
+        Assert.Same(real, pair.First);
+        Assert.Same(other, pair.Second);
+    }
+
+    [Fact]
+    public void FindOverlappingPairs_MatchesPartIntersectsOnASmallGrid()
+    {
+        // 10-wide squares on a 7 pitch: neighbors (diagonal ones too) overlap, squares two
+        // steps apart are clear, and one small square is contained in the middle one.
+        var parts = new List<Part>();
+        for (var row = 0; row < 3; row++)
+            for (var column = 0; column < 3; column++)
+                parts.Add(TestHelpers.MakePartAt(column * 7, row * 7, 10));
+        parts.Add(TestHelpers.MakePartAt(11, 11, 2));
+
+        var expected = new List<(int, int)>();
+        for (var i = 0; i < parts.Count; i++)
+            for (var j = i + 1; j < parts.Count; j++)
+                if (parts[i].Intersects(parts[j], out _))
+                    expected.Add((i, j));
+
+        var actual = PartOverlapChecker.FindOverlappingPairs(parts)
+            .Select(pair => (parts.IndexOf(pair.First), parts.IndexOf(pair.Second)))
+            .ToList();
+
+        Assert.Contains((0, 1), expected);
+        Assert.DoesNotContain((0, 2), expected);
+        Assert.Contains((4, 9), expected);
+        Assert.Equal(expected, actual);
+    }
+
     private static long Bits(double value) => BitConverter.DoubleToInt64Bits(value);
 
     private static long[] PolygonBits(Polygon polygon) => new[]

docs/geometry/visual-overlap-check.md

@@ -91,9 +91,11 @@ material), even if the dialog is later canceled. There is no check during export
 
 `OpenNest.Diagnostics.PlateOverlapAnalyzer` in OpenNest.Core checks a group of placed
 parts and returns the shared material for each overlapping pair as connected
-islands. It clips with Clipper2. Existing `Part.Intersects`, `PartOverlapChecker`,
-`Plate.HasOverlappingParts`, engine validators, and CLI entry points are unchanged
-and still use the hand-written `Collision` kernel (its GPU port is on hold).
+islands. It clips with Clipper2. Existing `Part.Intersects`, `PartOverlapChecker` and
+engine validators are unchanged and still use the hand-written `Collision` kernel (its
+GPU port is on hold). The console's overlap check and the MCP `check_overlaps` tool list
+overlapping pairs through `PartOverlapChecker.FindOverlappingPairs`, which skips cut-off
+parts and reports a contained or stacked part even though no outlines cross.
 
 ## Synchronous use