24 files changed, 492 insertions, 115 deletions

diff --git a/src/WixToolset.Core.Burn/BurnBackendErrors.cs b/src/WixToolset.Core.Burn/BurnBackendErrors.cs
index f23db47d..854c84e0 100644
--- a/src/WixToolset.Core.Burn/BurnBackendErrors.cs
+++ b/src/WixToolset.Core.Burn/BurnBackendErrors.cs
@@ -67,6 +67,6 @@ namespace WixToolset.Core.Burn
             PackageCachePayloadCollision = 8006,
             PackageCachePayloadCollision2 = 8007,
             MultipleAttachedContainersUnsupported = 8008,
-        }
+        } // last available is 8499. 8500 is BurnBackendWarnings.
     }
 }
diff --git a/src/WixToolset.Core.Burn/BurnBackendWarnings.cs b/src/WixToolset.Core.Burn/BurnBackendWarnings.cs
index 5edbbd67..a0ffa1dc 100644
--- a/src/WixToolset.Core.Burn/BurnBackendWarnings.cs
+++ b/src/WixToolset.Core.Burn/BurnBackendWarnings.cs
@@ -31,6 +31,6 @@ namespace WixToolset.Core.Burn
             AttachedContainerPayloadCollision = 8500,
             AttachedContainerPayloadCollision2 = 8501,
             EmptyContainer = 8502,
-        }
+        } // last available is 8999. 9000 is VerboseMessages.
     }
 }
diff --git a/src/WixToolset.Core.WindowsInstaller/WindowsInstallerBackendErrors.cs b/src/WixToolset.Core.WindowsInstaller/WindowsInstallerBackendErrors.cs
index c1232dcc..0c15ad05 100644
--- a/src/WixToolset.Core.WindowsInstaller/WindowsInstallerBackendErrors.cs
+++ b/src/WixToolset.Core.WindowsInstaller/WindowsInstallerBackendErrors.cs
@@ -18,7 +18,7 @@ namespace WixToolset.Core.WindowsInstaller
 
         public enum Ids
         {
-            // ReplaceThisWithTheFirstError = 7000,
-        }
+            // ReplaceThisWithTheFirstError = 7500,
+        } // last available is 7999. 8000 is BurnBackendErrors.
     }
 }
diff --git a/src/WixToolset.Core.WindowsInstaller/WindowsInstallerBackendWarnings.cs b/src/WixToolset.Core.WindowsInstaller/WindowsInstallerBackendWarnings.cs
index 0eaadbe1..d0986a4d 100644
--- a/src/WixToolset.Core.WindowsInstaller/WindowsInstallerBackendWarnings.cs
+++ b/src/WixToolset.Core.WindowsInstaller/WindowsInstallerBackendWarnings.cs
@@ -18,7 +18,7 @@ namespace WixToolset.Core.WindowsInstaller
 
         public enum Ids
         {
-            // ReplaceThisWithTheFirstWarning = 7500,
-        }
+            // ReplaceThisWithTheFirstWarning = 7100,
+        } // last available is 7499. 7500 is WindowsInstallerBackendErrors.
     }
 }
diff --git a/src/WixToolset.Core/CompilerErrors.cs b/src/WixToolset.Core/CompilerErrors.cs
index 9b3d85b9..10646dfd 100644
--- a/src/WixToolset.Core/CompilerErrors.cs
+++ b/src/WixToolset.Core/CompilerErrors.cs
@@ -38,6 +38,6 @@ namespace WixToolset.Core
 
             IllegalName = 6601,
             ExampleRegid = 6602,
-        }
+        } // 5400-5499 and 6600-6699 were the ranges for Dependency and Tag which are now in Core between CompilerWarnings and CompilerErrors.
     }
 }
diff --git a/src/WixToolset.Core/CompilerWarnings.cs b/src/WixToolset.Core/CompilerWarnings.cs
index eb838ae2..5c11b878 100644
--- a/src/WixToolset.Core/CompilerWarnings.cs
+++ b/src/WixToolset.Core/CompilerWarnings.cs
@@ -60,6 +60,6 @@ namespace WixToolset.Core
             Win64Component = 5435,
             DirectoryRefStandardDirectoryDeprecated = 5436,
             DefiningStandardDirectoryDeprecated = 5437,
-        }
+        } // 5400-5499 and 6600-6699 were the ranges for Dependency and Tag which are now in Core between CompilerWarnings and CompilerErrors.
     }
 }
diff --git a/src/WixToolset.Core/Compiler_Bundle.cs b/src/WixToolset.Core/Compiler_Bundle.cs
index 779ad376..e09246df 100644
--- a/src/WixToolset.Core/Compiler_Bundle.cs
+++ b/src/WixToolset.Core/Compiler_Bundle.cs
@@ -2375,6 +2375,7 @@ namespace WixToolset.Core
                 }
 
                 this.CreateChainPackageMetaRows(sourceLineNumbers, parentType, parentId, ComplexReferenceChildType.Package, id.Id, previousType, previousId, after);
+                this.Core.CreateGroupAndOrderingRows(sourceLineNumbers, parentType, parentId, ComplexReferenceChildType.ContainerPackage, id.Id, ComplexReferenceChildType.Unknown, null);
             }
 
             return id.Id;
diff --git a/src/WixToolset.Core/Link/FlattenAndProcessBundleTablesCommand.cs b/src/WixToolset.Core/Link/FlattenAndProcessBundleTablesCommand.cs
index 0fa48d8c..e8df25ed 100644
--- a/src/WixToolset.Core/Link/FlattenAndProcessBundleTablesCommand.cs
+++ b/src/WixToolset.Core/Link/FlattenAndProcessBundleTablesCommand.cs
@@ -42,46 +42,143 @@ namespace WixToolset.Core.Link
             // We need to flatten the nested PayloadGroups and PackageGroups under
             // UX, Chain, and any Containers. When we're done, the WixGroups table
             // will hold Payloads under UX, ChainPackages (references?) under Chain,
-            // and ChainPackages/Payloads under the attached and any detatched
-            // Containers.
+            // and ContainerPackages/Payloads under any authored Containers.
             var groups = new WixGroupingOrdering(this.EntrySection, this.Messaging);
 
-            // Create UX payloads and Package payloads
+            // Create UX payloads and Package payloads and Container packages
             groups.UseTypes(new[] { ComplexReferenceParentType.Container, ComplexReferenceParentType.Layout, ComplexReferenceParentType.PackageGroup, ComplexReferenceParentType.PayloadGroup, ComplexReferenceParentType.Package },
-                            new[] { ComplexReferenceChildType.PackageGroup, ComplexReferenceChildType.Package, ComplexReferenceChildType.PackagePayload, ComplexReferenceChildType.PayloadGroup, ComplexReferenceChildType.Payload });
+                            new[] { ComplexReferenceChildType.ContainerPackage, ComplexReferenceChildType.PackageGroup, ComplexReferenceChildType.Package, ComplexReferenceChildType.PackagePayload, ComplexReferenceChildType.PayloadGroup, ComplexReferenceChildType.Payload });
             groups.FlattenAndRewriteGroups(ComplexReferenceParentType.Package, false);
             groups.FlattenAndRewriteGroups(ComplexReferenceParentType.Container, false);
             groups.FlattenAndRewriteGroups(ComplexReferenceParentType.Layout, false);
 
             // Create Chain packages...
             groups.UseTypes(new[] { ComplexReferenceParentType.PackageGroup }, new[] { ComplexReferenceChildType.Package, ComplexReferenceChildType.PackageGroup });
-            groups.FlattenAndRewriteRows(ComplexReferenceChildType.PackageGroup, "WixChain", false);
+            groups.FlattenAndRewriteRows(ComplexReferenceParentType.PackageGroup, "WixChain", false);
 
             groups.RemoveUsedGroupRows();
         }
 
         private void ProcessBundleComplexReferences()
         {
+            var containersById = this.EntrySection.Symbols.OfType<WixBundleContainerSymbol>().ToDictionary(c => c.Id.Id);
             var groups = this.EntrySection.Symbols.OfType<WixGroupSymbol>().ToList();
             var payloadsById = this.EntrySection.Symbols.OfType<WixBundlePayloadSymbol>().ToDictionary(c => c.Id.Id);
 
+            var containerByPackage = new Dictionary<string, WixBundleContainerSymbol>();
+            var referencedPackages = new HashSet<string>();
+            var payloadsInBA = new HashSet<string>();
+            var payloadsInPackageOrLayout = new HashSet<string>();
+
+            foreach (var groupSymbol in groups)
+            {
+                switch (groupSymbol.ChildType)
+                {
+                    case ComplexReferenceChildType.ContainerPackage:
+                        switch (groupSymbol.ParentType)
+                        {
+                            case ComplexReferenceParentType.Container:
+                                if (containerByPackage.TryGetValue(groupSymbol.ChildId, out var collisionContainer))
+                                {
+                                    this.Messaging.Write(LinkerErrors.PackageInMultipleContainers(groupSymbol.SourceLineNumbers, groupSymbol.ChildId, groupSymbol.ParentId, collisionContainer.Id.Id));
+                                }
+                                else
+                                {
+                                    containerByPackage.Add(groupSymbol.ChildId, containersById[groupSymbol.ParentId]);
+                                }
+                                break;
+                        }
+                        break;
+                    case ComplexReferenceChildType.Package:
+                        switch (groupSymbol.ParentType)
+                        {
+                            case ComplexReferenceParentType.PackageGroup:
+                                if (groupSymbol.ParentId == "WixChain")
+                                {
+                                    referencedPackages.Add(groupSymbol.ChildId);
+                                }
+                                break;
+                        }
+                        break;
+                    case ComplexReferenceChildType.Payload:
+                        switch (groupSymbol.ParentType)
+                        {
+                            case ComplexReferenceParentType.Container:
+                                if (groupSymbol.ParentId == BurnConstants.BurnUXContainerName)
+                                {
+                                    payloadsInBA.Add(groupSymbol.ChildId);
+                                }
+                                break;
+                            case ComplexReferenceParentType.Layout:
+                                payloadsById[groupSymbol.ChildId].LayoutOnly = true;
+                                payloadsInPackageOrLayout.Add(groupSymbol.ChildId);
+                                break;
+                            case ComplexReferenceParentType.Package:
+                                payloadsInPackageOrLayout.Add(groupSymbol.ChildId);
+                                break;
+                        }
+                        break;
+                }
+            }
+
+            foreach (var package in this.EntrySection.Symbols.OfType<WixBundlePackageSymbol>())
+            {
+                if (!referencedPackages.Contains(package.Id.Id))
+                {
+                    this.Messaging.Write(LinkerErrors.UnscheduledChainPackage(package.SourceLineNumbers, package.Id.Id));
+                }
+            }
+
+            foreach (var rollbackBoundary in this.EntrySection.Symbols.OfType<WixBundleRollbackBoundarySymbol>())
+            {
+                if (!referencedPackages.Contains(rollbackBoundary.Id.Id))
+                {
+                    this.Messaging.Write(LinkerErrors.UnscheduledRollbackBoundary(rollbackBoundary.SourceLineNumbers, rollbackBoundary.Id.Id));
+                }
+            }
+
+            foreach (var payload in payloadsById.Values)
+            {
+                var payloadId = payload.Id.Id;
+                if (payloadsInBA.Contains(payloadId))
+                {
+                    if (payloadsInPackageOrLayout.Contains(payloadId))
+                    {
+                        this.Messaging.Write(LinkerErrors.PayloadSharedWithBA(payload.SourceLineNumbers, payloadId));
+                    }
+                }
+                else if (!payloadsInPackageOrLayout.Contains(payloadId))
+                {
+                    this.Messaging.Write(LinkerErrors.OrphanedPayload(payload.SourceLineNumbers, payloadId));
+                }
+            }
+
+            if (this.Messaging.EncounteredError)
+            {
+                return;
+            }
+
             // Assign authored payloads to authored containers.
             // Compressed Payloads not assigned to a container here will get assigned to the default attached container during binding.
             foreach (var groupSymbol in groups)
             {
-                if (ComplexReferenceChildType.Payload == groupSymbol.ChildType)
+                if (groupSymbol.ChildType == ComplexReferenceChildType.Payload && groupSymbol.ParentType == ComplexReferenceParentType.Container)
                 {
                     var payloadSymbol = payloadsById[groupSymbol.ChildId];
+                    var containerId = groupSymbol.ParentId;
 
-                    if (ComplexReferenceParentType.Container == groupSymbol.ParentType)
+                    if (String.IsNullOrEmpty(payloadSymbol.ContainerRef))
+                    {
+                        payloadSymbol.ContainerRef = containerId;
+                    }
+                    else
                     {
-                        // TODO: v3 didn't warn if we overwrote the payload's container.
-                        // Should we warn now?
-                        payloadSymbol.ContainerRef = groupSymbol.ParentId;
+                        this.Messaging.Write(LinkerWarnings.PayloadInMultipleContainers(groupSymbol.SourceLineNumbers, groupSymbol.ChildId, containerId, payloadSymbol.ContainerRef));
                     }
-                    else if (ComplexReferenceParentType.Layout == groupSymbol.ParentType)
+
+                    if (payloadSymbol.LayoutOnly)
                     {
-                        payloadSymbol.LayoutOnly = true;
+                        this.Messaging.Write(LinkerWarnings.LayoutPayloadInContainer(groupSymbol.SourceLineNumbers, groupSymbol.ChildId, containerId));
                     }
                 }
             }
diff --git a/src/WixToolset.Core/Link/WixGroupingOrdering.cs b/src/WixToolset.Core/Link/WixGroupingOrdering.cs
index 99220900..f9de82a9 100644
--- a/src/WixToolset.Core/Link/WixGroupingOrdering.cs
+++ b/src/WixToolset.Core/Link/WixGroupingOrdering.cs
@@ -62,7 +62,7 @@ namespace WixToolset.Core.Link
         /// <param name="parentType">The group type for the parent group to flatten.</param>
         /// <param name="parentId">The identifier of the parent group to flatten.</param>
         /// <param name="removeUsedRows">Whether to remove used group rows before returning.</param>
-        public void FlattenAndRewriteRows(ComplexReferenceChildType parentType, string parentId, bool removeUsedRows)
+        public void FlattenAndRewriteRows(ComplexReferenceParentType parentType, string parentId, bool removeUsedRows)
         {
             var parentTypeString = parentType.ToString();
             Debug.Assert(this.groupTypes.Contains(parentTypeString));
@@ -648,14 +648,11 @@ namespace WixToolset.Core.Link
             // We *don't* propagate ordering information from Packages or
             // Containers to their children, because ordering doesn't matter
             // for them, and a Payload in two Packages (or Containers) can
-            // cause a circular reference to occur.  We do, however, need to
-            // track the ordering in the UX Container, because we need the
-            // first payload to be the entrypoint.
+            // cause a circular reference to occur.
             private bool ShouldItemPropagateChildOrdering()
             {
-                if (String.Equals(nameof(ComplexReferenceChildType.Package), this.Type, StringComparison.Ordinal) ||
-                    (String.Equals(nameof(ComplexReferenceParentType.Container), this.Type, StringComparison.Ordinal) &&
-                    !String.Equals(BurnConstants.BurnUXContainerName, this.Id, StringComparison.Ordinal)))
+                if (String.Equals(nameof(ComplexReferenceParentType.Package), this.Type, StringComparison.Ordinal) ||
+                    String.Equals(nameof(ComplexReferenceParentType.Container), this.Type, StringComparison.Ordinal))
                 {
                     return false;
                 }
diff --git a/src/WixToolset.Core/LinkerErrors.cs b/src/WixToolset.Core/LinkerErrors.cs
new file mode 100644
index 00000000..7ce8c00e
--- /dev/null
+++ b/src/WixToolset.Core/LinkerErrors.cs
@@ -0,0 +1,48 @@
+// Copyright (c) .NET Foundation and contributors. All rights reserved. Licensed under the Microsoft Reciprocal License. See LICENSE.TXT file in the project root for full license information.
+
+namespace WixToolset.Core
+{
+    using WixToolset.Data;
+
+    internal static class LinkerErrors
+    {
+        public static Message OrphanedPayload(SourceLineNumber sourceLineNumbers, string payloadId)
+        {
+            return Message(sourceLineNumbers, Ids.OrphanedPayload, "Found orphaned Payload '{0}'. Make sure to reference it from a Package, the BootstrapperApplication, or the Bundle or move it into its own Fragment so it only gets linked in when actually used.", payloadId);
+        }
+
+        public static Message PackageInMultipleContainers(SourceLineNumber sourceLineNumbers, string packageId, string containerId1, string containerId2)
+        {
+            return Message(sourceLineNumbers, Ids.PackageInMultipleContainers, "The Package '{0}' is referenced from multiple containers - Container '{1}' and Container '{2}'. This is not currently supported.", packageId, containerId1, containerId2);
+        }
+
+        public static Message PayloadSharedWithBA(SourceLineNumber sourceLineNumbers, string payloadId)
+        {
+            return Message(sourceLineNumbers, Ids.PayloadSharedWithBA, "The Payload '{0}' is shared with the BootstrapperApplication. This is not currently supported.", payloadId);
+        }
+
+        public static Message UnscheduledChainPackage(SourceLineNumber sourceLineNumbers, string packageId)
+        {
+            return Message(sourceLineNumbers, Ids.UnscheduledChainPackage, "Found orphaned Package '{0}'. Make sure to reference it from the Chain or move it into its own Fragment so it only gets linked in when actually used.", packageId);
+        }
+
+        public static Message UnscheduledRollbackBoundary(SourceLineNumber sourceLineNumbers, string rollbackBoundaryId)
+        {
+            return Message(sourceLineNumbers, Ids.UnscheduledRollbackBoundary, "Found orphaned RollbackBoundary '{0}'. Make sure to reference it from the Chain or move it into its own Fragment so it only gets linked in when actually used.", rollbackBoundaryId);
+        }
+
+        private static Message Message(SourceLineNumber sourceLineNumber, Ids id, string format, params object[] args)
+        {
+            return new Message(sourceLineNumber, MessageLevel.Error, (int)id, format, args);
+        }
+
+        public enum Ids
+        {
+            OrphanedPayload = 7000,
+            PackageInMultipleContainers = 7001,
+            PayloadSharedWithBA = 7002,
+            UnscheduledChainPackage = 7003,
+            UnscheduledRollbackBoundary = 7004,
+        } // last available is 7099. 7100 is WindowsInstallerBackendWarnings.
+    }
+}
diff --git a/src/WixToolset.Core/LinkerWarnings.cs b/src/WixToolset.Core/LinkerWarnings.cs
new file mode 100644
index 00000000..0eca090e
--- /dev/null
+++ b/src/WixToolset.Core/LinkerWarnings.cs
@@ -0,0 +1,30 @@
+// Copyright (c) .NET Foundation and contributors. All rights reserved. Licensed under the Microsoft Reciprocal License. See LICENSE.TXT file in the project root for full license information.
+
+namespace WixToolset.Core
+{
+    using WixToolset.Data;
+
+    internal static class LinkerWarnings
+    {
+        public static Message LayoutPayloadInContainer(SourceLineNumber sourceLineNumbers, string payloadId, string containerId)
+        {
+            return Message(sourceLineNumbers, Ids.LayoutPayloadInContainer, "The layout-only Payload '{0}' is being added to Container '{1}'. It will not be extracted during layout.", payloadId, containerId);
+        }
+
+        public static Message PayloadInMultipleContainers(SourceLineNumber sourceLineNumbers, string payloadId, string containerId1, string containerId2)
+        {
+            return Message(sourceLineNumbers, Ids.PayloadInMultipleContainers, "The Payload '{0}' can't be added to Container '{1}' because it was already added to Container '{2}'.", payloadId, containerId1, containerId2);
+        }
+
+        private static Message Message(SourceLineNumber sourceLineNumber, Ids id, string format, params object[] args)
+        {
+            return new Message(sourceLineNumber, MessageLevel.Warning, (int)id, format, args);
+        }
+
+        public enum Ids
+        {
+            LayoutPayloadInContainer = 6900,
+            PayloadInMultipleContainers = 6901,
+        } // last available is 6999. 7000 is LinkerErrors.
+    }
+}
diff --git a/src/WixToolset.Core/WixToolset.Core.csproj b/src/WixToolset.Core/WixToolset.Core.csproj
index 902f63ce..7242d500 100644
--- a/src/WixToolset.Core/WixToolset.Core.csproj
+++ b/src/WixToolset.Core/WixToolset.Core.csproj
@@ -14,6 +14,18 @@
   </PropertyGroup>
 
   <ItemGroup>
+    <AssemblyAttribute Include="System.Runtime.CompilerServices.InternalsVisibleTo">
+      <_Parameter1>WixToolset.Core.TestPackage, PublicKey=0024000004800000940000000602000000240000525341310004000001000100a9967ec28982f42ee51a47dd5204315975a6ed69294b982146a99a70130a2fa13e226aaddde14c17d1bf3af69e8956d69a86585e74d208efcc5ac98a0686055327b2e87960d3c39bf3a6bc1e572863327d19dbf4fd2616dda124dbea260755a2d1d39d3cf1049ea526493eb2bf996b8ad985e3012308529e5b9b0f5cd5fa04bd</_Parameter1>
+    </AssemblyAttribute>
+    <AssemblyAttribute Include="System.Runtime.CompilerServices.InternalsVisibleTo">
+      <_Parameter1>WixToolsetTest.Core.Burn, PublicKey=0024000004800000940000000602000000240000525341310004000001000100a9967ec28982f42ee51a47dd5204315975a6ed69294b982146a99a70130a2fa13e226aaddde14c17d1bf3af69e8956d69a86585e74d208efcc5ac98a0686055327b2e87960d3c39bf3a6bc1e572863327d19dbf4fd2616dda124dbea260755a2d1d39d3cf1049ea526493eb2bf996b8ad985e3012308529e5b9b0f5cd5fa04bd</_Parameter1>
+    </AssemblyAttribute>
+    <AssemblyAttribute Include="System.Runtime.CompilerServices.InternalsVisibleTo">
+      <_Parameter1>WixToolsetTest.CoreIntegration, PublicKey=0024000004800000940000000602000000240000525341310004000001000100a9967ec28982f42ee51a47dd5204315975a6ed69294b982146a99a70130a2fa13e226aaddde14c17d1bf3af69e8956d69a86585e74d208efcc5ac98a0686055327b2e87960d3c39bf3a6bc1e572863327d19dbf4fd2616dda124dbea260755a2d1d39d3cf1049ea526493eb2bf996b8ad985e3012308529e5b9b0f5cd5fa04bd</_Parameter1>
+    </AssemblyAttribute>
+  </ItemGroup>
+
+  <ItemGroup>
     <PackageReference Include="WixToolset.Data" Version="4.0.*" />
     <PackageReference Include="WixToolset.Extensibility" Version="4.0.*" />
     <PackageReference Include="WixToolset.Core.Native" Version="4.0.*" />
diff --git a/src/test/WixToolsetTest.CoreIntegration/BundleFixture.cs b/src/test/WixToolsetTest.CoreIntegration/BundleFixture.cs
index cc91d212..ab644080 100644
--- a/src/test/WixToolsetTest.CoreIntegration/BundleFixture.cs
+++ b/src/test/WixToolsetTest.CoreIntegration/BundleFixture.cs
@@ -10,6 +10,7 @@ namespace WixToolsetTest.CoreIntegration
     using System.Xml;
     using Example.Extension;
     using WixBuildTools.TestSupport;
+    using WixToolset.Core;
     using WixToolset.Core.Burn;
     using WixToolset.Core.TestPackage;
     using WixToolset.Data;
@@ -368,7 +369,61 @@ namespace WixToolsetTest.CoreIntegration
             }
         }
 
-        [Fact(Skip = "https://github.com/wixtoolset/issues/issues/6291")]
+        [Fact]
+        public void CantBuildWithOrphanPayload()
+        {
+            var folder = TestData.Get(@"TestData");
+
+            using (var fs = new DisposableFileSystem())
+            {
+                var baseFolder = fs.GetFolder();
+                var intermediateFolder = Path.Combine(baseFolder, "obj");
+                var exePath = Path.Combine(baseFolder, @"bin\test.exe");
+
+                var result = WixRunner.Execute(new[]
+                {
+                    "build",
+                    Path.Combine(folder, "BadInput", "OrphanPayload.wxs"),
+                    Path.Combine(folder, "BundleWithPackageGroupRef", "Bundle.wxs"),
+                    Path.Combine(folder, "BundleWithPackageGroupRef", "MinimalPackageGroup.wxs"),
+                    "-bindpath", Path.Combine(folder, "SimpleBundle", "data"),
+                    "-bindpath", Path.Combine(folder, ".Data"),
+                    "-intermediateFolder", intermediateFolder,
+                    "-o", exePath,
+                });
+
+                Assert.Equal((int)LinkerErrors.Ids.OrphanedPayload, result.ExitCode);
+            }
+        }
+
+        [Fact]
+        public void CantBuildWithPackageInMultipleContainers()
+        {
+            var folder = TestData.Get(@"TestData");
+
+            using (var fs = new DisposableFileSystem())
+            {
+                var baseFolder = fs.GetFolder();
+                var intermediateFolder = Path.Combine(baseFolder, "obj");
+                var exePath = Path.Combine(baseFolder, @"bin\test.exe");
+
+                var result = WixRunner.Execute(new[]
+                {
+                    "build",
+                    Path.Combine(folder, "BadInput", "PackageInMultipleContainers.wxs"),
+                    Path.Combine(folder, "BundleWithPackageGroupRef", "Bundle.wxs"),
+                    Path.Combine(folder, "BundleWithPackageGroupRef", "MinimalPackageGroup.wxs"),
+                    "-bindpath", Path.Combine(folder, "SimpleBundle", "data"),
+                    "-bindpath", Path.Combine(folder, ".Data"),
+                    "-intermediateFolder", intermediateFolder,
+                    "-o", exePath,
+                });
+
+                Assert.Equal((int)LinkerErrors.Ids.PackageInMultipleContainers, result.ExitCode);
+            }
+        }
+
+        [Fact]
         public void CantBuildWithUnscheduledPackage()
         {
             var folder = TestData.Get(@"TestData");
@@ -390,11 +445,11 @@ namespace WixToolsetTest.CoreIntegration
                     "-o", exePath,
                 });
 
-                Assert.InRange(result.ExitCode, 2, Int32.MaxValue);
+                Assert.Equal((int)LinkerErrors.Ids.UnscheduledChainPackage, result.ExitCode);
             }
         }
 
-        [Fact(Skip = "https://github.com/wixtoolset/issues/issues/6291")]
+        [Fact]
         public void CantBuildWithUnscheduledRollbackBoundary()
         {
             var folder = TestData.Get(@"TestData");
@@ -416,7 +471,7 @@ namespace WixToolsetTest.CoreIntegration
                     "-o", exePath,
                 });
 
-                Assert.InRange(result.ExitCode, 2, Int32.MaxValue);
+                Assert.Equal((int)LinkerErrors.Ids.UnscheduledRollbackBoundary, result.ExitCode);
             }
         }
     }
diff --git a/src/test/WixToolsetTest.CoreIntegration/BundleManifestFixture.cs b/src/test/WixToolsetTest.CoreIntegration/BundleManifestFixture.cs
index 4a8473df..29c741dc 100644
--- a/src/test/WixToolsetTest.CoreIntegration/BundleManifestFixture.cs
+++ b/src/test/WixToolsetTest.CoreIntegration/BundleManifestFixture.cs
@@ -291,7 +291,7 @@ namespace WixToolsetTest.CoreIntegration
                 var baFolderPath = Path.Combine(baseFolder, "ba");
                 var extractFolderPath = Path.Combine(baseFolder, "extract");
 
-                var result = WixRunner.Execute(false, new[]
+                var result = WixRunner.Execute(new[]
                 {
                     "build",
                     Path.Combine(folder, "SharedPayloadsBetweenPackages", "SharedPayloadsBetweenPackages.wxs"),
@@ -315,8 +315,8 @@ namespace WixToolsetTest.CoreIntegration
                     { "ExePackage", new List<string> { "CacheId", "InstallSize", "Size" } },
                 };
                 Assert.Equal(2, exePackageElements.Count);
-                Assert.Equal("<ExePackage Id='credwiz.exe' Cache='keep' CacheId='*' InstallSize='*' Size='*' PerMachine='yes' Permanent='yes' Vital='yes' RollbackBoundaryForward='WixDefaultBoundary' LogPathVariable='WixBundleLog_credwiz.exe' RollbackLogPathVariable='WixBundleRollbackLog_credwiz.exe' DetectCondition='' InstallArguments='' UninstallArguments='' RepairArguments='' Repairable='no'><PayloadRef Id='credwiz.exe' /><PayloadRef Id='SourceFilePayload' /></ExePackage>", exePackageElements[0].GetTestXml(ignoreAttributesByElementName));
-                Assert.Equal("<ExePackage Id='cscript.exe' Cache='keep' CacheId='*' InstallSize='*' Size='*' PerMachine='yes' Permanent='yes' Vital='yes' RollbackBoundaryBackward='WixDefaultBoundary' LogPathVariable='WixBundleLog_cscript.exe' RollbackLogPathVariable='WixBundleRollbackLog_cscript.exe' DetectCondition='' InstallArguments='' UninstallArguments='' RepairArguments='' Repairable='no'><PayloadRef Id='cscript.exe' /><PayloadRef Id='SourceFilePayload' /></ExePackage>", exePackageElements[1].GetTestXml(ignoreAttributesByElementName));
+                Assert.Equal("<ExePackage Id='credwiz.exe' Cache='keep' CacheId='*' InstallSize='*' Size='*' PerMachine='yes' Permanent='yes' Vital='yes' RollbackBoundaryForward='WixDefaultBoundary' LogPathVariable='WixBundleLog_credwiz.exe' RollbackLogPathVariable='WixBundleRollbackLog_credwiz.exe' DetectCondition='none' InstallArguments='' UninstallArguments='' RepairArguments='' Repairable='no'><PayloadRef Id='credwiz.exe' /><PayloadRef Id='SourceFilePayload' /></ExePackage>", exePackageElements[0].GetTestXml(ignoreAttributesByElementName));
+                Assert.Equal("<ExePackage Id='cscript.exe' Cache='keep' CacheId='*' InstallSize='*' Size='*' PerMachine='yes' Permanent='yes' Vital='yes' RollbackBoundaryBackward='WixDefaultBoundary' LogPathVariable='WixBundleLog_cscript.exe' RollbackLogPathVariable='WixBundleRollbackLog_cscript.exe' DetectCondition='none' InstallArguments='' UninstallArguments='' RepairArguments='' Repairable='no'><PayloadRef Id='cscript.exe' /><PayloadRef Id='SourceFilePayload' /></ExePackage>", exePackageElements[1].GetTestXml(ignoreAttributesByElementName));
             }
         }
 
diff --git a/src/test/WixToolsetTest.CoreIntegration/ContainerFixture.cs b/src/test/WixToolsetTest.CoreIntegration/ContainerFixture.cs
index f24429f7..ffeda069 100644
--- a/src/test/WixToolsetTest.CoreIntegration/ContainerFixture.cs
+++ b/src/test/WixToolsetTest.CoreIntegration/ContainerFixture.cs
@@ -8,10 +8,9 @@ namespace WixToolsetTest.CoreIntegration
     using System.Linq;
     using System.Xml;
     using WixBuildTools.TestSupport;
+    using WixToolset.Core;
     using WixToolset.Core.Burn;
     using WixToolset.Core.TestPackage;
-    using WixToolset.Data;
-    using WixToolset.Data.Symbols;
     using Xunit;
 
     public class ContainerFixture
@@ -30,33 +29,9 @@ namespace WixToolsetTest.CoreIntegration
                 var baFolderPath = Path.Combine(baseFolder, "ba");
                 var extractFolderPath = Path.Combine(baseFolder, "extract");
 
-                var result = WixRunner.Execute(new[]
-                {
-                    "build",
-                    Path.Combine(folder, "MsiTransaction", "FirstX86.wxs"),
-                    Path.Combine(folder, "ProductWithComponentGroupRef", "MinimalComponentGroup.wxs"),
-                    Path.Combine(folder, "ProductWithComponentGroupRef", "Product.wxs"),
-                    "-bindpath", Path.Combine(folder, "SingleFile", "data"),
-                    "-intermediateFolder", intermediateFolder,
-                    "-o", Path.Combine(binFolder, "FirstX86.msi"),
-                });
-
-                result.AssertSuccess();
+                this.BuildMsis(folder, intermediateFolder, binFolder);
 
-                result = WixRunner.Execute(new[]
-                {
-                    "build",
-                    Path.Combine(folder, "MsiTransaction", "FirstX64.wxs"),
-                    Path.Combine(folder, "ProductWithComponentGroupRef", "MinimalComponentGroup.wxs"),
-                    Path.Combine(folder, "ProductWithComponentGroupRef", "Product.wxs"),
-                    "-bindpath", Path.Combine(folder, "SingleFile", "data"),
-                    "-intermediateFolder", intermediateFolder,
-                    "-o", Path.Combine(binFolder, "FirstX64.msi"),
-                });
-
-                result.AssertSuccess();
-
-                result = WixRunner.Execute(new[]
+                var result = WixRunner.Execute(new[]
                 {
                     "build",
                     Path.Combine(folder, "Container", "HarvestIntoDetachedContainer.wxs"),
@@ -98,33 +73,9 @@ namespace WixToolsetTest.CoreIntegration
                 var baFolderPath = Path.Combine(baseFolder, "ba");
                 var extractFolderPath = Path.Combine(baseFolder, "extract");
 
-                var result = WixRunner.Execute(new[]
-                {
-                    "build",
-                    Path.Combine(folder, "MsiTransaction", "FirstX86.wxs"),
-                    Path.Combine(folder, "ProductWithComponentGroupRef", "MinimalComponentGroup.wxs"),
-                    Path.Combine(folder, "ProductWithComponentGroupRef", "Product.wxs"),
-                    "-bindpath", Path.Combine(folder, "SingleFile", "data"),
-                    "-intermediateFolder", intermediateFolder,
-                    "-o", Path.Combine(binFolder, "FirstX86.msi"),
-                });
-
-                result.AssertSuccess();
-
-                result = WixRunner.Execute(new[]
-                {
-                    "build",
-                    Path.Combine(folder, "MsiTransaction", "FirstX64.wxs"),
-                    Path.Combine(folder, "ProductWithComponentGroupRef", "MinimalComponentGroup.wxs"),
-                    Path.Combine(folder, "ProductWithComponentGroupRef", "Product.wxs"),
-                    "-bindpath", Path.Combine(folder, "SingleFile", "data"),
-                    "-intermediateFolder", intermediateFolder,
-                    "-o", Path.Combine(binFolder, "FirstX64.msi"),
-                });
-
-                result.AssertSuccess();
+                this.BuildMsis(folder, intermediateFolder, binFolder);
 
-                result = WixRunner.Execute(new[]
+                var result = WixRunner.Execute(new[]
                 {
                     "build",
                     Path.Combine(folder, "Container", "HarvestIntoDetachedContainer.wxs"),
@@ -174,7 +125,7 @@ namespace WixToolsetTest.CoreIntegration
         }
 
         [Fact]
-        public void MultipleAttachedContainersAreNotCurrentlySupported()
+        public void LayoutPayloadIsPutInContainer()
         {
             var folder = TestData.Get(@"TestData");
 
@@ -187,36 +138,92 @@ namespace WixToolsetTest.CoreIntegration
                 var baFolderPath = Path.Combine(baseFolder, "ba");
                 var extractFolderPath = Path.Combine(baseFolder, "extract");
 
-                var result = WixRunner.Execute(new[]
+                this.BuildMsis(folder, intermediateFolder, binFolder);
+
+                var result = WixRunner.Execute(false, new[]
                 {
                     "build",
-                    Path.Combine(folder, "MsiTransaction", "FirstX86.wxs"),
-                    Path.Combine(folder, "ProductWithComponentGroupRef", "MinimalComponentGroup.wxs"),
-                    Path.Combine(folder, "ProductWithComponentGroupRef", "Product.wxs"),
-                    "-bindpath", Path.Combine(folder, "SingleFile", "data"),
+                    Path.Combine(folder, "Container", "LayoutPayloadInContainer.wxs"),
+                    "-bindpath", Path.Combine(folder, "SimpleBundle", "data"),
+                    "-bindpath", binFolder,
                     "-intermediateFolder", intermediateFolder,
-                    "-o", Path.Combine(binFolder, "FirstX86.msi"),
+                    "-o", bundlePath
                 });
 
+                WixAssert.CompareLineByLine(new string[]
+                {
+                    "The layout-only Payload 'SharedPayload' is being added to Container 'FirstX64'. It will not be extracted during layout.",
+                }, result.Messages.Select(m => m.ToString()).ToArray());
                 result.AssertSuccess();
 
-                result = WixRunner.Execute(new[]
+                Assert.True(File.Exists(bundlePath));
+
+                var extractResult = BundleExtractor.ExtractBAContainer(null, bundlePath, baFolderPath, extractFolderPath);
+                extractResult.AssertSuccess();
+
+                var ignoreAttributes = new Dictionary<string, List<string>> { { "Payload", new List<string> { "FileSize", "Hash" } } };
+                var payloads = extractResult.SelectManifestNodes("/burn:BurnManifest/burn:Payload[@Id='SharedPayload']")
+                                            .Cast<XmlElement>()
+                                            .Select(e => e.GetTestXml(ignoreAttributes))
+                                            .ToArray();
+                WixAssert.CompareLineByLine(new string[]
+                {
+                    "<Payload Id='SharedPayload' FilePath='LayoutPayloadInContainer.wxs' FileSize='*' Hash='*' LayoutOnly='yes' Packaging='embedded' SourcePath='a1' Container='FirstX64' />",
+                }, payloads);
+            }
+        }
+
+        [Fact]
+        public void MultipleAttachedContainersAreNotCurrentlySupported()
+        {
+            var folder = TestData.Get(@"TestData");
+
+            using (var fs = new DisposableFileSystem())
+            {
+                var baseFolder = fs.GetFolder();
+                var intermediateFolder = Path.Combine(baseFolder, "obj");
+                var binFolder = Path.Combine(baseFolder, "bin");
+                var bundlePath = Path.Combine(binFolder, "test.exe");
+                var baFolderPath = Path.Combine(baseFolder, "ba");
+                var extractFolderPath = Path.Combine(baseFolder, "extract");
+
+                this.BuildMsis(folder, intermediateFolder, binFolder);
+
+                var result = WixRunner.Execute(new[]
                 {
                     "build",
-                    Path.Combine(folder, "MsiTransaction", "FirstX64.wxs"),
-                    Path.Combine(folder, "ProductWithComponentGroupRef", "MinimalComponentGroup.wxs"),
-                    Path.Combine(folder, "ProductWithComponentGroupRef", "Product.wxs"),
-                    "-bindpath", Path.Combine(folder, "SingleFile", "data"),
+                    Path.Combine(folder, "Container", "MultipleAttachedContainers.wxs"),
+                    Path.Combine(folder, "BundleWithPackageGroupRef", "Bundle.wxs"),
+                    "-bindpath", Path.Combine(folder, "SimpleBundle", "data"),
+                    "-bindpath", binFolder,
                     "-intermediateFolder", intermediateFolder,
-                    "-o", Path.Combine(binFolder, "FirstX64.msi"),
+                    "-o", bundlePath
                 });
 
-                result.AssertSuccess();
+                Assert.Equal((int)BurnBackendErrors.Ids.MultipleAttachedContainersUnsupported, result.ExitCode);
+            }
+        }
+
+        [Fact]
+        public void PayloadIsNotPutInMultipleContainers()
+        {
+            var folder = TestData.Get(@"TestData");
+
+            using (var fs = new DisposableFileSystem())
+            {
+                var baseFolder = fs.GetFolder();
+                var intermediateFolder = Path.Combine(baseFolder, "obj");
+                var binFolder = Path.Combine(baseFolder, "bin");
+                var bundlePath = Path.Combine(binFolder, "test.exe");
+                var baFolderPath = Path.Combine(baseFolder, "ba");
+                var extractFolderPath = Path.Combine(baseFolder, "extract");
+
+                this.BuildMsis(folder, intermediateFolder, binFolder);
 
-                result = WixRunner.Execute(new[]
+                var result = WixRunner.Execute(false, new[]
                 {
                     "build",
-                    Path.Combine(folder, "Container", "MultipleAttachedContainers.wxs"),
+                    Path.Combine(folder, "Container", "PayloadInMultipleContainers.wxs"),
                     Path.Combine(folder, "BundleWithPackageGroupRef", "Bundle.wxs"),
                     "-bindpath", Path.Combine(folder, "SimpleBundle", "data"),
                     "-bindpath", binFolder,
@@ -224,8 +231,56 @@ namespace WixToolsetTest.CoreIntegration
                     "-o", bundlePath
                 });
 
-                Assert.Equal((int)BurnBackendErrors.Ids.MultipleAttachedContainersUnsupported, result.ExitCode);
+                WixAssert.CompareLineByLine(new string[]
+                {
+                    "The Payload 'SharedPayload' can't be added to Container 'FirstX64' because it was already added to Container 'FirstX86'.",
+                }, result.Messages.Select(m => m.ToString()).ToArray());
+                result.AssertSuccess();
+
+                Assert.True(File.Exists(bundlePath));
+
+                var extractResult = BundleExtractor.ExtractBAContainer(null, bundlePath, baFolderPath, extractFolderPath);
+                extractResult.AssertSuccess();
+
+                var ignoreAttributes = new Dictionary<string, List<string>> { { "Payload", new List<string> { "FileSize", "Hash" } } };
+                var payloads = extractResult.SelectManifestNodes("/burn:BurnManifest/burn:Payload[@Id='SharedPayload']")
+                                            .Cast<XmlElement>()
+                                            .Select(e => e.GetTestXml(ignoreAttributes))
+                                            .ToArray();
+                WixAssert.CompareLineByLine(new string[]
+                {
+                    "<Payload Id='SharedPayload' FilePath='PayloadInMultipleContainers.wxs' FileSize='*' Hash='*' Packaging='embedded' SourcePath='a2' Container='FirstX86' />",
+                }, payloads);
             }
         }
+
+        private void BuildMsis(string folder, string intermediateFolder, string binFolder)
+        {
+            var result = WixRunner.Execute(new[]
+            {
+                "build",
+                Path.Combine(folder, "MsiTransaction", "FirstX86.wxs"),
+                Path.Combine(folder, "ProductWithComponentGroupRef", "MinimalComponentGroup.wxs"),
+                Path.Combine(folder, "ProductWithComponentGroupRef", "Product.wxs"),
+                "-bindpath", Path.Combine(folder, "SingleFile", "data"),
+                "-intermediateFolder", intermediateFolder,
+                "-o", Path.Combine(binFolder, "FirstX86.msi"),
+            });
+
+            result.AssertSuccess();
+
+            result = WixRunner.Execute(new[]
+            {
+                "build",
+                Path.Combine(folder, "MsiTransaction", "FirstX64.wxs"),
+                Path.Combine(folder, "ProductWithComponentGroupRef", "MinimalComponentGroup.wxs"),
+                Path.Combine(folder, "ProductWithComponentGroupRef", "Product.wxs"),
+                "-bindpath", Path.Combine(folder, "SingleFile", "data"),
+                "-intermediateFolder", intermediateFolder,
+                "-o", Path.Combine(binFolder, "FirstX64.msi"),
+            });
+
+            result.AssertSuccess();
+        }
     }
 }
diff --git a/src/test/WixToolsetTest.CoreIntegration/PayloadFixture.cs b/src/test/WixToolsetTest.CoreIntegration/PayloadFixture.cs
index e9e59b9e..da87bf6c 100644
--- a/src/test/WixToolsetTest.CoreIntegration/PayloadFixture.cs
+++ b/src/test/WixToolsetTest.CoreIntegration/PayloadFixture.cs
@@ -8,6 +8,7 @@ namespace WixToolsetTest.CoreIntegration
     using System.Linq;
     using System.Xml;
     using WixBuildTools.TestSupport;
+    using WixToolset.Core;
     using WixToolset.Core.TestPackage;
     using WixToolset.Data;
     using WixToolset.Data.Symbols;
@@ -117,7 +118,7 @@ namespace WixToolsetTest.CoreIntegration
             }
         }
 
-        [Fact(Skip = "https://github.com/wixtoolset/issues/issues/5273")]
+        [Fact]
         public void RejectsPayloadSharedBetweenPackageAndBA()
         {
             var folder = TestData.Get(@"TestData");
@@ -139,7 +140,7 @@ namespace WixToolsetTest.CoreIntegration
                     "-o", bundlePath,
                 });
 
-                Assert.InRange(result.ExitCode, 2, int.MaxValue);
+                Assert.Equal((int)LinkerErrors.Ids.PayloadSharedWithBA, result.ExitCode);
             }
         }
 
diff --git a/src/test/WixToolsetTest.CoreIntegration/TestData/BadInput/OrphanPayload.wxs b/src/test/WixToolsetTest.CoreIntegration/TestData/BadInput/OrphanPayload.wxs
new file mode 100644
index 00000000..92a9602f
--- /dev/null
+++ b/src/test/WixToolsetTest.CoreIntegration/TestData/BadInput/OrphanPayload.wxs
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="utf-8"?>
+<Wix xmlns="http://wixtoolset.org/schemas/v4/wxs">
+    <Fragment>
+        <PackageGroup Id="BundlePackages">
+            <PackageGroupRef Id="MinimalPackageGroup"  />
+        </PackageGroup>
+        <PayloadGroup Id="OrphanPayloads">
+            <Payload Id="OrphanPayload" SourceFile="$(sys.SOURCEFILEPATH)" />
+        </PayloadGroup>
+    </Fragment>
+</Wix>
diff --git a/src/test/WixToolsetTest.CoreIntegration/TestData/BadInput/PackageInMultipleContainers.wxs b/src/test/WixToolsetTest.CoreIntegration/TestData/BadInput/PackageInMultipleContainers.wxs
new file mode 100644
index 00000000..a00874ce
--- /dev/null
+++ b/src/test/WixToolsetTest.CoreIntegration/TestData/BadInput/PackageInMultipleContainers.wxs
@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="utf-8"?>
+<Wix xmlns="http://wixtoolset.org/schemas/v4/wxs">
+    <Fragment>
+        <PackageGroup Id="BundlePackages">
+            <PackageGroupRef Id="MinimalPackageGroup" />
+        </PackageGroup>
+        <Container Id="First">
+            <PackageGroupRef Id="BundlePackages" />
+        </Container>
+        <Container Id="Second">
+            <PackageGroupRef Id="BundlePackages" />
+        </Container>
+    </Fragment>
+</Wix>
diff --git a/src/test/WixToolsetTest.CoreIntegration/TestData/BadInput/UnscheduledPackage.wxs b/src/test/WixToolsetTest.CoreIntegration/TestData/BadInput/UnscheduledPackage.wxs
index ab86982d..fc53c4a2 100644
--- a/src/test/WixToolsetTest.CoreIntegration/TestData/BadInput/UnscheduledPackage.wxs
+++ b/src/test/WixToolsetTest.CoreIntegration/TestData/BadInput/UnscheduledPackage.wxs
@@ -2,15 +2,15 @@
 <Wix xmlns="http://wixtoolset.org/schemas/v4/wxs">
     <Fragment>
         <PackageGroup Id="BundlePackages">
-            <ExePackage Id="Auto1" SourceFile="burn.exe" CacheId="Auto1" />
-            <ExePackage Id="Auto2" SourceFile="burn.exe" CacheId="Auto2" />
+            <ExePackage Id="Auto1" SourceFile="burn.exe" CacheId="Auto1" DetectCondition="none" />
+            <ExePackage Id="Auto2" SourceFile="burn.exe" CacheId="Auto2" DetectCondition="none" />
         </PackageGroup>
         <SetVariableRef Id="Dummy" />
     </Fragment>
     <Fragment>
         <SetVariable Id="Dummy" Variable="Dummy" />
         <PackageGroup Id="Unscheduled">
-            <ExePackage Id="Unscheduled1" SourceFile="burn.exe" CacheId="Unscheduled1" />
+            <ExePackage Id="Unscheduled1" SourceFile="burn.exe" CacheId="Unscheduled1" DetectCondition="none" />
         </PackageGroup>
     </Fragment>
 </Wix>
diff --git a/src/test/WixToolsetTest.CoreIntegration/TestData/BadInput/UnscheduledRollbackBoundary.wxs b/src/test/WixToolsetTest.CoreIntegration/TestData/BadInput/UnscheduledRollbackBoundary.wxs
index 8015ed92..6cf8528e 100644
--- a/src/test/WixToolsetTest.CoreIntegration/TestData/BadInput/UnscheduledRollbackBoundary.wxs
+++ b/src/test/WixToolsetTest.CoreIntegration/TestData/BadInput/UnscheduledRollbackBoundary.wxs
@@ -2,8 +2,8 @@
 <Wix xmlns="http://wixtoolset.org/schemas/v4/wxs">
     <Fragment>
         <PackageGroup Id="BundlePackages">
-            <ExePackage Id="Auto1" SourceFile="burn.exe" CacheId="Auto1" />
-            <ExePackage Id="Auto2" SourceFile="burn.exe" CacheId="Auto2" />
+            <ExePackage Id="Auto1" SourceFile="burn.exe" CacheId="Auto1" DetectCondition="none" />
+            <ExePackage Id="Auto2" SourceFile="burn.exe" CacheId="Auto2" DetectCondition="none" />
         </PackageGroup>
         <SetVariableRef Id="Dummy" />
     </Fragment>
diff --git a/src/test/WixToolsetTest.CoreIntegration/TestData/Container/LayoutPayloadInContainer.wxs b/src/test/WixToolsetTest.CoreIntegration/TestData/Container/LayoutPayloadInContainer.wxs
new file mode 100644
index 00000000..0c5f8c7e
--- /dev/null
+++ b/src/test/WixToolsetTest.CoreIntegration/TestData/Container/LayoutPayloadInContainer.wxs
@@ -0,0 +1,28 @@
+<?xml version="1.0" encoding="utf-8"?>
+<Wix xmlns="http://wixtoolset.org/schemas/v4/wxs">
+    <Bundle Name="BurnBundle" Version="1.0.0.0" Manufacturer="Example Corporation" UpgradeCode="{B5B23622-239B-4E3B-BDAB-67648CB975BF}">
+        <BootstrapperApplication>
+            <BootstrapperApplicationDll SourceFile="fakeba.dll" />
+        </BootstrapperApplication>
+        <Chain>
+            <PackageGroupRef Id="BundlePackages" />
+        </Chain>
+        <PayloadGroupRef Id="Shared" />
+    </Bundle>
+    <Fragment>
+        <PackageGroup Id="BundlePackages">
+            <PackageGroupRef Id="FirstX64" />
+        </PackageGroup>
+        <PackageGroup Id="FirstX64">
+            <MsiPackage SourceFile="FirstX64.msi">
+                <PayloadGroupRef Id="Shared" />
+            </MsiPackage>
+        </PackageGroup>
+        <Container Id="FirstX64" Name="FirstX64" Type="detached">
+            <PackageGroupRef Id="FirstX64" />
+        </Container>
+        <PayloadGroup Id="Shared">
+            <Payload Id="SharedPayload" SourceFile="$(sys.SOURCEFILEPATH)" />
+        </PayloadGroup>
+    </Fragment>
+</Wix>
diff --git a/src/test/WixToolsetTest.CoreIntegration/TestData/Container/PayloadInMultipleContainers.wxs b/src/test/WixToolsetTest.CoreIntegration/TestData/Container/PayloadInMultipleContainers.wxs
new file mode 100644
index 00000000..c7f549a3
--- /dev/null
+++ b/src/test/WixToolsetTest.CoreIntegration/TestData/Container/PayloadInMultipleContainers.wxs
@@ -0,0 +1,28 @@
+<?xml version="1.0" encoding="utf-8"?>
+<Wix xmlns="http://wixtoolset.org/schemas/v4/wxs">
+    <Fragment>
+        <PackageGroup Id="BundlePackages">
+            <PackageGroupRef Id="FirstX86" />
+            <PackageGroupRef Id="FirstX64" />
+        </PackageGroup>
+        <PackageGroup Id="FirstX86">
+            <MsiPackage SourceFile="FirstX86.msi">
+                <PayloadGroupRef Id="Shared" />
+            </MsiPackage>
+        </PackageGroup>
+        <PackageGroup Id="FirstX64">
+            <MsiPackage SourceFile="FirstX64.msi">
+                <PayloadGroupRef Id="Shared" />
+            </MsiPackage>
+        </PackageGroup>
+        <Container Id="FirstX86" Name="FirstX86" Type="detached">
+            <PackageGroupRef Id="FirstX86" />
+        </Container>
+        <Container Id="FirstX64" Name="FirstX64" Type="detached">
+            <PackageGroupRef Id="FirstX64" />
+        </Container>
+        <PayloadGroup Id="Shared">
+            <Payload Id="SharedPayload" SourceFile="$(sys.SOURCEFILEPATH)" />
+        </PayloadGroup>
+    </Fragment>
+</Wix>
diff --git a/src/test/WixToolsetTest.CoreIntegration/TestData/Payload/SharedBAAndPackagePayloadBundle.wxs b/src/test/WixToolsetTest.CoreIntegration/TestData/Payload/SharedBAAndPackagePayloadBundle.wxs
index 4cfeb99f..5263cbd4 100644
--- a/src/test/WixToolsetTest.CoreIntegration/TestData/Payload/SharedBAAndPackagePayloadBundle.wxs
+++ b/src/test/WixToolsetTest.CoreIntegration/TestData/Payload/SharedBAAndPackagePayloadBundle.wxs
@@ -2,7 +2,7 @@
 <Wix xmlns="http://wixtoolset.org/schemas/v4/wxs">
     <Fragment>
         <PackageGroup Id="BundlePackages">
-            <ExePackage SourceFile="burn.exe">
+            <ExePackage SourceFile="burn.exe" DetectCondition="none">
                 <PayloadGroupRef Id="Shared" />
             </ExePackage>
         </PackageGroup>
diff --git a/src/test/WixToolsetTest.CoreIntegration/TestData/SharedPayloadsBetweenPackages/SharedPayloadsBetweenPackages.wxs b/src/test/WixToolsetTest.CoreIntegration/TestData/SharedPayloadsBetweenPackages/SharedPayloadsBetweenPackages.wxs
index 3457a3b7..f16fce0d 100644
--- a/src/test/WixToolsetTest.CoreIntegration/TestData/SharedPayloadsBetweenPackages/SharedPayloadsBetweenPackages.wxs
+++ b/src/test/WixToolsetTest.CoreIntegration/TestData/SharedPayloadsBetweenPackages/SharedPayloadsBetweenPackages.wxs
@@ -2,10 +2,10 @@
 <Wix xmlns="http://wixtoolset.org/schemas/v4/wxs">
     <Fragment>
         <PackageGroup Id="BundlePackages">
-            <ExePackage SourceFile="C:\Windows\system32\credwiz.exe" Permanent="yes">
+            <ExePackage SourceFile="C:\Windows\system32\credwiz.exe" Permanent="yes" DetectCondition="none">
                 <PayloadGroupRef Id="SharedPayloads" />
             </ExePackage>
-            <ExePackage SourceFile="C:\Windows\system32\cscript.exe" Permanent="yes">
+            <ExePackage SourceFile="C:\Windows\system32\cscript.exe" Permanent="yes" DetectCondition="none">
                 <PayloadGroupRef Id="SharedPayloads" />
             </ExePackage>
         </PackageGroup>