8 files changed, 206 insertions, 21 deletions

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.*" />