Update to WixOutput file structure to fix embedded file handling

21 files changed, 243 insertions, 140 deletions

diff --git a/src/WixToolset.Core.Burn/Bind/BindBundleCommand.cs b/src/WixToolset.Core.Burn/Bind/BindBundleCommand.cs
index 6b4b9d68..c2164744 100644
--- a/src/WixToolset.Core.Burn/Bind/BindBundleCommand.cs
+++ b/src/WixToolset.Core.Burn/Bind/BindBundleCommand.cs
@@ -462,7 +462,7 @@ namespace WixToolset.Core.Burn
             this.TrackedFiles = trackedFiles;
 
             // TODO: Eventually this gets removed
-            var intermediate = new Intermediate(this.Output.Id, new[] { section }, this.Output.Localizations.ToDictionary(l => l.Culture, StringComparer.OrdinalIgnoreCase), this.Output.EmbedFilePaths);
+            var intermediate = new Intermediate(this.Output.Id, new[] { section }, this.Output.Localizations.ToDictionary(l => l.Culture, StringComparer.OrdinalIgnoreCase));
             var trackIntermediate = this.BackendHelper.TrackFile(Path.Combine(this.IntermediateFolder, Path.GetFileName(Path.ChangeExtension(this.OutputPath, "wir"))), TrackedFileType.Intermediate);
             intermediate.Save(trackIntermediate.Path);
             trackedFiles.Add(trackIntermediate);
diff --git a/src/WixToolset.Core.Burn/Bundles/ProcessPayloadsCommand.cs b/src/WixToolset.Core.Burn/Bundles/ProcessPayloadsCommand.cs
index 0560e336..17251143 100644
--- a/src/WixToolset.Core.Burn/Bundles/ProcessPayloadsCommand.cs
+++ b/src/WixToolset.Core.Burn/Bundles/ProcessPayloadsCommand.cs
@@ -56,7 +56,7 @@ namespace WixToolset.Core.Burn.Bundles
                 // Embedded files (aka: files from binary .wixlibs) are not content files (because they are hidden
                 // in the .wixlib).
                 var sourceFile = payload.SourceFile;
-                payload.ContentFile = !sourceFile.EmbeddedFileIndex.HasValue;
+                payload.ContentFile = !sourceFile.Embed;
 
                 this.UpdatePayloadPackagingType(payload);
 
diff --git a/src/WixToolset.Core.TestPackage/WixRunner.cs b/src/WixToolset.Core.TestPackage/WixRunner.cs
index ab5045fa..d2202328 100644
--- a/src/WixToolset.Core.TestPackage/WixRunner.cs
+++ b/src/WixToolset.Core.TestPackage/WixRunner.cs
@@ -16,7 +16,7 @@ namespace WixToolset.Core.TestPackage
             return Execute(args, serviceProvider, out messages);
         }
 
-        public static WixRunnerResult Execute(string[] args)
+        public static WixRunnerResult Execute(params string[] args)
         {
             var serviceProvider = new WixToolsetServiceProvider();
             var exitCode = Execute(args, serviceProvider, out var messages);
diff --git a/src/WixToolset.Core.WindowsInstaller/Bind/BindDatabaseCommand.cs b/src/WixToolset.Core.WindowsInstaller/Bind/BindDatabaseCommand.cs
index 411f64bf..3e4806a7 100644
--- a/src/WixToolset.Core.WindowsInstaller/Bind/BindDatabaseCommand.cs
+++ b/src/WixToolset.Core.WindowsInstaller/Bind/BindDatabaseCommand.cs
@@ -17,11 +17,13 @@ namespace WixToolset.Core.WindowsInstaller.Bind
     /// <summary>
     /// Binds a databse.
     /// </summary>
-    internal class BindDatabaseCommand
+    internal class BindDatabaseCommand : IDisposable
     {
         // As outlined in RFC 4122, this is our namespace for generating name-based (version 3) UUIDs.
         internal static readonly Guid WixComponentGuidNamespace = new Guid("{3064E5C6-FB63-4FE9-AC49-E446A792EFA5}");
 
+        private bool disposed;
+
         public BindDatabaseCommand(IBindContext context, IEnumerable<IWindowsInstallerBackendBinderExtension> backendExtension, Validator validator)
         {
             this.ServiceProvider = context.ServiceProvider;
@@ -92,7 +94,7 @@ namespace WixToolset.Core.WindowsInstaller.Bind
 
         public IEnumerable<ITrackedFile> TrackedFiles { get; private set; }
 
-        public Pdb Pdb { get; private set; }
+        public WixOutput Wixout { get; private set; }
 
         public void Execute()
         {
@@ -524,29 +526,41 @@ namespace WixToolset.Core.WindowsInstaller.Bind
                 trackedFiles.AddRange(command.TrackedFiles);
             }
 
-            this.Pdb = new Pdb { Output = output };
-
-            if (!String.IsNullOrEmpty(this.OutputPdbPath))
-            {
-                var trackPdb = this.BackendHelper.TrackFile(this.OutputPdbPath, TrackedFileType.Final);
-                trackedFiles.Add(trackPdb);
-
-                this.Pdb.Save(trackPdb.Path);
-            }
+            this.Wixout = this.CreateWixout(trackedFiles, this.Intermediate, output);
 
             this.FileTransfers = fileTransfers;
             // TODO: this is not sufficient to collect all Input files (for example, it misses Binary and Icon tables).
-            trackedFiles.AddRange(fileFacades.Select(f => this.BackendHelper.TrackFile(f.File.Source.Path, TrackedFileType.Input, f.File.SourceLineNumbers))); 
+            trackedFiles.AddRange(fileFacades.Select(f => this.BackendHelper.TrackFile(f.File.Source.Path, TrackedFileType.Input, f.File.SourceLineNumbers)));
             this.TrackedFiles = trackedFiles;
 
             // TODO: Eventually this gets removed
-            var intermediate = new Intermediate(this.Intermediate.Id, new[] { section }, this.Intermediate.Localizations.ToDictionary(l => l.Culture, StringComparer.OrdinalIgnoreCase), this.Intermediate.EmbedFilePaths);
+            var intermediate = new Intermediate(this.Intermediate.Id, new[] { section }, this.Intermediate.Localizations.ToDictionary(l => l.Culture, StringComparer.OrdinalIgnoreCase));
             var trackIntermediate = this.BackendHelper.TrackFile(Path.Combine(this.IntermediateFolder, Path.GetFileName(Path.ChangeExtension(this.OutputPath, "wir"))), TrackedFileType.Intermediate);
             intermediate.Save(trackIntermediate.Path);
             trackedFiles.Add(trackIntermediate);
+        }
 
-            //transfer = this.BackendHelper.CreateFileTransfer(intermediatePath, Path.ChangeExtension(this.OutputPath, "wir"), true, FileTransferType.Built);
-            //fileTransfers.Add(transfer);
+        private WixOutput CreateWixout(List<ITrackedFile> trackedFiles, Intermediate intermediate, Output output)
+        {
+            WixOutput wixout;
+
+            if (String.IsNullOrEmpty(this.OutputPdbPath))
+            {
+                wixout = WixOutput.Create();
+            }
+            else
+            {
+                var trackPdb = this.BackendHelper.TrackFile(this.OutputPdbPath, TrackedFileType.Final);
+                trackedFiles.Add(trackPdb);
+
+                wixout = WixOutput.Create(trackPdb.Path);
+            }
+
+            intermediate.Save(wixout);
+
+            output.Save(wixout);
+
+            return wixout;
         }
 
 #if TODO_FINISH_PATCH
@@ -934,5 +948,27 @@ namespace WixToolset.Core.WindowsInstaller.Bind
 
             return command.GeneratedTemporaryFiles;
         }
+
+        #region IDisposable Support
+
+        public void Dispose()
+        {
+            this.Dispose(true);
+        }
+
+        protected virtual void Dispose(bool disposing)
+        {
+            if (!this.disposed)
+            {
+                if (disposing)
+                {
+                    this.Wixout?.Dispose();
+                }
+
+                this.disposed = true;
+            }
+        }
+
+        #endregion
     }
 }
diff --git a/src/WixToolset.Core.WindowsInstaller/MsiBackend.cs b/src/WixToolset.Core.WindowsInstaller/MsiBackend.cs
index 2ebb3f13..5cd7204a 100644
--- a/src/WixToolset.Core.WindowsInstaller/MsiBackend.cs
+++ b/src/WixToolset.Core.WindowsInstaller/MsiBackend.cs
@@ -2,7 +2,6 @@
 
 namespace WixToolset.Core.WindowsInstaller
 {
-    using System;
     using WixToolset.Core.WindowsInstaller.Bind;
     using WixToolset.Core.WindowsInstaller.Inscribe;
     using WixToolset.Core.WindowsInstaller.Unbind;
@@ -26,18 +25,21 @@ namespace WixToolset.Core.WindowsInstaller
 
             var validator = Validator.CreateFromContext(context, "darice.cub");
 
-            var command = new BindDatabaseCommand(context, backendExtensions, validator);
-            command.Execute();
+            using (var command = new BindDatabaseCommand(context, backendExtensions, validator))
+            {
+                command.Execute();
 
-            var result = context.ServiceProvider.GetService<IBindResult>();
-            result.FileTransfers = command.FileTransfers;
-            result.TrackedFiles = command.TrackedFiles;
+                var result = context.ServiceProvider.GetService<IBindResult>();
+                result.FileTransfers = command.FileTransfers;
+                result.TrackedFiles = command.TrackedFiles;
 
-            foreach (var extension in backendExtensions)
-            {
-                extension.PostBackendBind(result, command.Pdb);
+                foreach (var extension in backendExtensions)
+                {
+                    extension.PostBackendBind(result, command.Wixout);
+                }
+
+                return result;
             }
-            return result;
         }
 
         public IDecompileResult Decompile(IDecompileContext context)
diff --git a/src/WixToolset.Core.WindowsInstaller/MsmBackend.cs b/src/WixToolset.Core.WindowsInstaller/MsmBackend.cs
index d5281759..f048b4e2 100644
--- a/src/WixToolset.Core.WindowsInstaller/MsmBackend.cs
+++ b/src/WixToolset.Core.WindowsInstaller/MsmBackend.cs
@@ -2,7 +2,6 @@
 
 namespace WixToolset.Core.WindowsInstaller
 {
-    using System;
     using WixToolset.Core.WindowsInstaller.Bind;
     using WixToolset.Core.WindowsInstaller.Unbind;
     using WixToolset.Data;
@@ -25,24 +24,21 @@ namespace WixToolset.Core.WindowsInstaller
 
             var validator = Validator.CreateFromContext(context, "mergemod.cub");
 
-            var command = new BindDatabaseCommand(context, backendExtensions, validator);
-            command.Execute();
+            using (var command = new BindDatabaseCommand(context, backendExtensions, validator))
+            {
+                command.Execute();
 
-            var result = context.ServiceProvider.GetService<IBindResult>();
-            result.FileTransfers = command.FileTransfers;
-            result.TrackedFiles = command.TrackedFiles;
+                var result = context.ServiceProvider.GetService<IBindResult>();
+                result.FileTransfers = command.FileTransfers;
+                result.TrackedFiles = command.TrackedFiles;
 
-            foreach (var extension in backendExtensions)
-            {
-                extension.PostBackendBind(result, command.Pdb);
-            }
+                foreach (var extension in backendExtensions)
+                {
+                    extension.PostBackendBind(result, command.Wixout);
+                }
 
-            if (!String.IsNullOrEmpty(context.OutputPdbPath))
-            {
-                command.Pdb?.Save(context.OutputPdbPath);
+                return result;
             }
-
-            return result;
         }
 
         public IDecompileResult Decompile(IDecompileContext context)
@@ -67,10 +63,7 @@ namespace WixToolset.Core.WindowsInstaller
             return result;
         }
 
-        public bool Inscribe(IInscribeContext context)
-        {
-            return false;
-        }
+        public bool Inscribe(IInscribeContext context) => false;
 
         public Intermediate Unbind(IUnbindContext context)
         {
diff --git a/src/WixToolset.Core/Bind/ExpectedExtractFile.cs b/src/WixToolset.Core/Bind/ExpectedExtractFile.cs
index afad12fc..b27cdfee 100644
--- a/src/WixToolset.Core/Bind/ExpectedExtractFile.cs
+++ b/src/WixToolset.Core/Bind/ExpectedExtractFile.cs
@@ -1,4 +1,4 @@
-// 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.
+// 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.Bind
 {
@@ -9,7 +9,7 @@ namespace WixToolset.Core.Bind
     {
         public Uri Uri { get; set; }
 
-        public int EmbeddedFileIndex { get; set; }
+        public string EmbeddedFileId { get; set; }
 
         public string OutputPath { get; set; }
     }
diff --git a/src/WixToolset.Core/Bind/ExtractEmbeddedFiles.cs b/src/WixToolset.Core/Bind/ExtractEmbeddedFiles.cs
index 644e5c63..35c8a2f0 100644
--- a/src/WixToolset.Core/Bind/ExtractEmbeddedFiles.cs
+++ b/src/WixToolset.Core/Bind/ExtractEmbeddedFiles.cs
@@ -15,7 +15,7 @@ namespace WixToolset.Core.Bind
     /// </summary>
     internal class ExtractEmbeddedFiles
     {
-        private Dictionary<Uri, SortedList<int, string>> filesWithEmbeddedFiles = new Dictionary<Uri, SortedList<int, string>>();
+        private readonly Dictionary<Uri, SortedList<string, string>> filesWithEmbeddedFiles = new Dictionary<Uri, SortedList<string, string>>();
 
         public IEnumerable<Uri> Uris => this.filesWithEmbeddedFiles.Keys;
 
@@ -23,28 +23,28 @@ namespace WixToolset.Core.Bind
         /// Adds an embedded file index to track and returns the path where the embedded file will be extracted. Duplicates will return the same extract path.
         /// </summary>
         /// <param name="uri">Uri to file containing the embedded files.</param>
-        /// <param name="embeddedFileIndex">Index of the embedded file to extract.</param>
-        /// <param name="tempPath">Path where temporary files should be placed.</param>
+        /// <param name="embeddedFileId">Id of the embedded file to extract.</param>
+        /// <param name="extractFolder">Folder where extracted files should be placed.</param>
         /// <returns>The extract path for the embedded file.</returns>
-        public string AddEmbeddedFileIndex(Uri uri, int embeddedFileIndex, string tempPath)
+        public string AddEmbeddedFileToExtract(Uri uri, string embeddedFileId, string extractFolder)
         {
             // If the uri to the file that contains the embedded file does not already have embedded files
             // being extracted, create the dictionary to track that.
             if (!this.filesWithEmbeddedFiles.TryGetValue(uri, out var extracts))
             {
-                extracts = new SortedList<int, string>();
+                extracts = new SortedList<string, string>(StringComparer.OrdinalIgnoreCase);
                 this.filesWithEmbeddedFiles.Add(uri, extracts);
             }
 
             // If the embedded file is not already tracked in the dictionary of extracts, add it.
-            if (!extracts.TryGetValue(embeddedFileIndex, out var extractPath))
+            if (!extracts.TryGetValue(embeddedFileId, out var extractPath))
             {
-                string localFileNameWithoutExtension = Path.GetFileNameWithoutExtension(uri.LocalPath);
-                string unique = this.HashUri(uri.AbsoluteUri);
-                string extractedName = String.Format(CultureInfo.InvariantCulture, @"{0}_{1}\{2}", localFileNameWithoutExtension, unique, embeddedFileIndex);
+                var localFileNameWithoutExtension = Path.GetFileNameWithoutExtension(uri.LocalPath);
+                var unique = this.HashUri(uri.AbsoluteUri);
+                var extractedName = String.Format(CultureInfo.InvariantCulture, @"{0}_{1}\{2}", localFileNameWithoutExtension, unique, embeddedFileId);
 
-                extractPath = Path.Combine(tempPath, extractedName);
-                extracts.Add(embeddedFileIndex, extractPath);
+                extractPath = Path.GetFullPath(Path.Combine(extractFolder, extractedName));
+                extracts.Add(embeddedFileId, extractPath);
             }
 
             return extractPath;
@@ -52,35 +52,39 @@ namespace WixToolset.Core.Bind
 
         public IEnumerable<ExpectedExtractFile> GetExpectedEmbeddedFiles()
         {
+            var files = new List<ExpectedExtractFile>();
+
             foreach (var uriWithExtracts in this.filesWithEmbeddedFiles)
             {
                 foreach (var extracts in uriWithExtracts.Value)
                 {
-                    yield return new ExpectedExtractFile
+                    files.Add(new ExpectedExtractFile
                     {
                         Uri = uriWithExtracts.Key,
-                        EmbeddedFileIndex = extracts.Key,
+                        EmbeddedFileId = extracts.Key,
                         OutputPath = extracts.Value,
-                    };
+                    });
                 }
             }
+
+            return files;
         }
 
         public IEnumerable<ExpectedExtractFile> GetExtractFilesForUri(Uri uri)
         {
             if (!this.filesWithEmbeddedFiles.TryGetValue(uri, out var extracts))
             {
-                extracts = new SortedList<int, string>();
+                extracts = new SortedList<string, string>(StringComparer.OrdinalIgnoreCase);
             }
 
-            return extracts.Select(e => new ExpectedExtractFile() { Uri = uri, EmbeddedFileIndex = e.Key, OutputPath = e.Value });
+            return extracts.Select(e => new ExpectedExtractFile { Uri = uri, EmbeddedFileId = e.Key, OutputPath = e.Value });
         }
 
         private string HashUri(string uri)
         {
             using (SHA1 sha1 = new SHA1CryptoServiceProvider())
             {
-                byte[] hash = sha1.ComputeHash(Encoding.UTF8.GetBytes(uri));
+                var hash = sha1.ComputeHash(Encoding.UTF8.GetBytes(uri));
                 return Convert.ToBase64String(hash).TrimEnd('=').Replace('+', '-').Replace('/', '_');
             }
         }
diff --git a/src/WixToolset.Core/Bind/ExtractEmbeddedFilesCommand.cs b/src/WixToolset.Core/Bind/ExtractEmbeddedFilesCommand.cs
index d82609db..683c3c50 100644
--- a/src/WixToolset.Core/Bind/ExtractEmbeddedFilesCommand.cs
+++ b/src/WixToolset.Core/Bind/ExtractEmbeddedFilesCommand.cs
@@ -2,10 +2,9 @@
 
 namespace WixToolset.Core.Bind
 {
+    using System;
     using System.Collections.Generic;
-    using System.IO;
     using System.Linq;
-    using System.Reflection;
     using WixToolset.Data;
     using WixToolset.Extensibility.Data;
 
@@ -26,41 +25,18 @@ namespace WixToolset.Core.Bind
             {
                 var baseUri = expectedEmbeddedFileByUri.Key;
 
-                Stream stream = null;
-                try
+                using (var wixout = WixOutput.Read(baseUri))
                 {
-                    // If the embedded files are stored in an assembly resource stream (usually
-                    // a .wixlib embedded in a WixExtension).
-                    if ("embeddedresource" == baseUri.Scheme)
-                    {
-                        var assemblyPath = Path.GetFullPath(baseUri.LocalPath);
-                        var resourceName = baseUri.Fragment.TrimStart('#');
-
-                        var assembly = Assembly.LoadFile(assemblyPath);
-                        stream = assembly.GetManifestResourceStream(resourceName);
-                    }
-                    else // normal file (usually a binary .wixlib on disk).
-                    {
-                        stream = File.OpenRead(baseUri.LocalPath);
-                    }
+                    var uniqueIds = new SortedSet<string>(StringComparer.OrdinalIgnoreCase);
 
-                    using (var fs = FileStructure.Read(stream))
+                    foreach (var embeddedFile in expectedEmbeddedFileByUri)
                     {
-                        var uniqueIndicies = new SortedSet<int>();
-
-                        foreach (var embeddedFile in expectedEmbeddedFileByUri)
+                        if (uniqueIds.Add(embeddedFile.EmbeddedFileId))
                         {
-                            if (uniqueIndicies.Add(embeddedFile.EmbeddedFileIndex))
-                            {
-                                fs.ExtractEmbeddedFile(embeddedFile.EmbeddedFileIndex, embeddedFile.OutputPath);
-                            }
+                            wixout.ExtractEmbeddedFile(embeddedFile.EmbeddedFileId, embeddedFile.OutputPath);
                         }
                     }
                 }
-                finally
-                {
-                    stream?.Close();
-                }
             }
         }
     }
diff --git a/src/WixToolset.Core/Bind/ResolveFieldsCommand.cs b/src/WixToolset.Core/Bind/ResolveFieldsCommand.cs
index 2c213402..19a26915 100644
--- a/src/WixToolset.Core/Bind/ResolveFieldsCommand.cs
+++ b/src/WixToolset.Core/Bind/ResolveFieldsCommand.cs
@@ -98,9 +98,9 @@ namespace WixToolset.Core.Bind
 #endif
 
                             // File is embedded and path to it was not modified above.
-                            if (objectField.EmbeddedFileIndex.HasValue && isDefault)
+                            if (isDefault && objectField.Embed)
                             {
-                                var extractPath = this.FilesWithEmbeddedFiles.AddEmbeddedFileIndex(objectField.BaseUri, objectField.EmbeddedFileIndex.Value, this.IntermediateFolder);
+                                var extractPath = this.FilesWithEmbeddedFiles.AddEmbeddedFileToExtract(objectField.BaseUri, objectField.Path, this.IntermediateFolder);
 
                                 // Set the path to the embedded file once where it will be extracted.
                                 field.Set(extractPath);
diff --git a/src/WixToolset.Core/CommandLine/BuildCommand.cs b/src/WixToolset.Core/CommandLine/BuildCommand.cs
index 972258fe..5ee60984 100644
--- a/src/WixToolset.Core/CommandLine/BuildCommand.cs
+++ b/src/WixToolset.Core/CommandLine/BuildCommand.cs
@@ -100,29 +100,38 @@ namespace WixToolset.Core.CommandLine
 
             if (this.OutputType == OutputType.Library)
             {
-                var wixlib = this.LibraryPhase(wixobjs, wxls, this.commandLine.BindFiles, this.commandLine.BindPaths);
-
-                if (!this.Messaging.EncounteredError)
+                using (new IntermediateFieldContext("wix.lib"))
                 {
-                    wixlib.Save(this.commandLine.OutputFile);
+                    var wixlib = this.LibraryPhase(wixobjs, wxls, this.commandLine.BindFiles, this.commandLine.BindPaths);
+
+                    if (!this.Messaging.EncounteredError)
+                    {
+                        wixlib.Save(this.commandLine.OutputFile);
+                    }
                 }
             }
             else
             {
-                if (wixipl == null)
-                {
-                    wixipl = this.LinkPhase(wixobjs, this.commandLine.LibraryFilePaths, creator);
-                }
-
-                if (!this.Messaging.EncounteredError)
+                using (new IntermediateFieldContext("wix.link"))
                 {
-                    if (this.OutputType == OutputType.IntermediatePostLink)
+                    if (wixipl == null)
                     {
-                        wixipl.Save(this.commandLine.OutputFile);
+                        wixipl = this.LinkPhase(wixobjs, this.commandLine.LibraryFilePaths, creator);
                     }
-                    else
+
+                    if (!this.Messaging.EncounteredError)
                     {
-                        this.BindPhase(wixipl, wxls, filterCultures, this.commandLine.CabCachePath, this.commandLine.BindPaths, this.commandLine.BurnStubPath);
+                        if (this.OutputType == OutputType.IntermediatePostLink)
+                        {
+                            wixipl.Save(this.commandLine.OutputFile);
+                        }
+                        else
+                        {
+                            using (new IntermediateFieldContext("wix.bind"))
+                            {
+                                this.BindPhase(wixipl, wxls, filterCultures, this.commandLine.CabCachePath, this.commandLine.BindPaths, this.commandLine.BurnStubPath);
+                            }
+                        }
                     }
                 }
             }
@@ -469,6 +478,7 @@ namespace WixToolset.Core.CommandLine
                             break;
                         }
 
+                        case "bf":
                         case "bindfiles":
                             this.BindFiles = true;
                             return true;
diff --git a/src/WixToolset.Core/Librarian.cs b/src/WixToolset.Core/Librarian.cs
index 3c1810ac..5c0fb302 100644
--- a/src/WixToolset.Core/Librarian.cs
+++ b/src/WixToolset.Core/Librarian.cs
@@ -56,14 +56,14 @@ namespace WixToolset.Core
                     return null;
                 }
 
-                var embedFilePaths = this.ResolveFilePathsToEmbed(context, sections);
+                this.ResolveFilePathsToEmbed(context, sections);
 
                 foreach (var section in sections)
                 {
                     section.LibraryId = context.LibraryId;
                 }
 
-                library = new Intermediate(context.LibraryId, sections, localizationsByCulture, embedFilePaths);
+                library = new Intermediate(context.LibraryId, sections, localizationsByCulture);
 
                 this.Validate(library);
             }
@@ -78,10 +78,8 @@ namespace WixToolset.Core
             return this.Messaging.EncounteredError ? null : library;
         }
 
-        private List<string> ResolveFilePathsToEmbed(ILibraryContext context, IEnumerable<IntermediateSection> sections)
+        private void ResolveFilePathsToEmbed(ILibraryContext context, IEnumerable<IntermediateSection> sections)
         {
-            var embedFilePaths = new List<string>();
-
             // Resolve paths to files that are to be embedded in the library.
             if (context.BindFiles)
             {
@@ -104,9 +102,7 @@ namespace WixToolset.Core
                             if (!String.IsNullOrEmpty(file))
                             {
                                 // File was successfully resolved so track the embedded index as the embedded file index.
-                                field.Set(new IntermediateFieldPathValue { EmbeddedFileIndex = embedFilePaths.Count });
-
-                                embedFilePaths.Add(file);
+                                field.Set(new IntermediateFieldPathValue { Embed = true, Path = file });
                             }
                             else
                             {
@@ -116,8 +112,6 @@ namespace WixToolset.Core
                     }
                 }
             }
-
-            return embedFilePaths;
         }
 
         private void Validate(Intermediate library)
diff --git a/src/WixToolset.Core/Linker.cs b/src/WixToolset.Core/Linker.cs
index 81696840..6ef252b7 100644
--- a/src/WixToolset.Core/Linker.cs
+++ b/src/WixToolset.Core/Linker.cs
@@ -564,7 +564,7 @@ namespace WixToolset.Core
                 var collate = new CollateLocalizationsCommand(this.Messaging, localizations);
                 var localizationsByCulture = collate.Execute();
 
-                intermediate = new Intermediate(resolvedSection.Id, new[] { resolvedSection }, localizationsByCulture, null);
+                intermediate = new Intermediate(resolvedSection.Id, new[] { resolvedSection }, localizationsByCulture);
 
 #if MOVE_TO_BACKEND
                 this.CheckOutputConsistency(output);
diff --git a/src/test/Example.Extension/Data/example.wir b/src/test/Example.Extension/Data/example.wir
index 8e32f901..d1ee8b90 100644
--- a/src/test/Example.Extension/Data/example.wir
+++ b/src/test/Example.Extension/Data/example.wir
diff --git a/src/test/WixToolsetTest.CoreIntegration/MsiFixture.cs b/src/test/WixToolsetTest.CoreIntegration/MsiFixture.cs
index d056a1d6..e201b61f 100644
--- a/src/test/WixToolsetTest.CoreIntegration/MsiFixture.cs
+++ b/src/test/WixToolsetTest.CoreIntegration/MsiFixture.cs
@@ -312,9 +312,8 @@ namespace WixToolsetTest.CoreIntegration
                 var pdbPath = Path.Combine(intermediateFolder, @"bin\test.wixpdb");
                 Assert.True(File.Exists(pdbPath));
 
-                var pdb = Pdb.Load(pdbPath, suppressVersionCheck: true);
-                Assert.NotNull(pdb);
-                Assert.NotNull(pdb.Output);
+                var output = Output.Load(pdbPath, suppressVersionCheck: true);
+                Assert.NotNull(output);
             }
         }
 
@@ -449,6 +448,74 @@ namespace WixToolsetTest.CoreIntegration
         }
 
         [Fact]
+        public void CanBuildBinaryWixlib()
+        {
+            var folder = TestData.Get(@"TestData\SingleFile");
+
+            using (var fs = new DisposableFileSystem())
+            {
+                var baseFolder = fs.GetFolder();
+                var intermediateFolder = Path.Combine(baseFolder, "obj");
+
+                var result = WixRunner.Execute(
+                    "build",
+                    Path.Combine(folder, "Package.wxs"),
+                    Path.Combine(folder, "PackageComponents.wxs"),
+                    "-loc", Path.Combine(folder, "Package.en-us.wxl"),
+                    "-bindpath", Path.Combine(folder, "data"),
+                    "-intermediateFolder", intermediateFolder,
+                    "-bindfiles",
+                    "-o", Path.Combine(baseFolder, @"bin\test.wixlib"));
+
+                result.AssertSuccess();
+
+                using (var wixout = WixOutput.Read(Path.Combine(baseFolder, @"bin\test.wixlib")))
+                {
+                    Assert.NotNull(wixout.GetDataStream("wix-ir.json"));
+
+                    var text = wixout.GetData("wix-ir/test.txt");
+                    Assert.Equal("This is test.txt.", text);
+                }
+            }
+        }
+
+        [Fact]
+        public void CanBuildBinaryWixlibWithCollidingFilenames()
+        {
+            var folder = TestData.Get(@"TestData\SameFileFolders");
+
+            using (var fs = new DisposableFileSystem())
+            {
+                var baseFolder = fs.GetFolder();
+                var intermediateFolder = Path.Combine(baseFolder, "obj");
+
+                var result = WixRunner.Execute(
+                    "build",
+                    Path.Combine(folder, "TestComponents.wxs"),
+                    "-bindpath", Path.Combine(folder, "data"),
+                    "-intermediateFolder", intermediateFolder,
+                    "-bindfiles",
+                    "-o", Path.Combine(baseFolder, @"bin\test.wixlib"));
+
+                result.AssertSuccess();
+
+                using (var wixout = WixOutput.Read(Path.Combine(baseFolder, @"bin\test.wixlib")))
+                {
+                    Assert.NotNull(wixout.GetDataStream("wix-ir.json"));
+
+                    var text = wixout.GetData("wix-ir/test.txt");
+                    Assert.Equal(@"This is a\test.txt.", text);
+
+                    var text2 = wixout.GetData("wix-ir/test.txt-1");
+                    Assert.Equal(@"This is b\test.txt.", text2);
+
+                    var text3 = wixout.GetData("wix-ir/test.txt-2");
+                    Assert.Equal(@"This is c\test.txt.", text3);
+                }
+            }
+        }
+
+        [Fact]
         public void CanBuildWithIncludePath()
         {
             var folder = TestData.Get(@"TestData\IncludePath");
@@ -459,8 +526,7 @@ namespace WixToolsetTest.CoreIntegration
                 var baseFolder = fs.GetFolder();
                 var intermediateFolder = Path.Combine(baseFolder, "obj");
 
-                var result = WixRunner.Execute(new[]
-                {
+                var result = WixRunner.Execute(
                     "build",
                     Path.Combine(folder, "Package.wxs"),
                     Path.Combine(folder, "PackageComponents.wxs"),
@@ -468,8 +534,7 @@ namespace WixToolsetTest.CoreIntegration
                     "-bindpath", bindpath,
                     "-intermediateFolder", intermediateFolder,
                     "-o", Path.Combine(baseFolder, @"bin\test.msi"),
-                    "-i", bindpath,
-                });
+                    "-i", bindpath);
 
                 result.AssertSuccess();
 
@@ -635,8 +700,8 @@ namespace WixToolsetTest.CoreIntegration
 
                 result.AssertSuccess();
 
-                var pdb = Pdb.Load(Path.Combine(baseFolder, @"bin\test.wixpdb"), false);
-                var caRows = pdb.Output.Tables["CustomAction"].Rows.Single();
+                var output = Output.Load(Path.Combine(baseFolder, @"bin\test.wixpdb"), false);
+                var caRows = output.Tables["CustomAction"].Rows.Single();
                 Assert.Equal("SetINSTALLLOCATION", caRows.FieldAsString(0));
                 Assert.Equal("51", caRows.FieldAsString(1));
                 Assert.Equal("INSTALLLOCATION", caRows.FieldAsString(2));
@@ -711,8 +776,8 @@ namespace WixToolsetTest.CoreIntegration
 
                 result.AssertSuccess();
 
-                var pdb = Pdb.Load(Path.Combine(intermediateFolder, @"bin\test.wixpdb"), false);
-                Assert.NotEmpty(pdb.Output.SubStorages);
+                var output = Output.Load(Path.Combine(intermediateFolder, @"bin\test.wixpdb"), false);
+                Assert.NotEmpty(output.SubStorages);
             }
         }
     }
diff --git a/src/test/WixToolsetTest.CoreIntegration/TestData/SameFileFolders/TestComponents.wxs b/src/test/WixToolsetTest.CoreIntegration/TestData/SameFileFolders/TestComponents.wxs
new file mode 100644
index 00000000..765e6778
--- /dev/null
+++ b/src/test/WixToolsetTest.CoreIntegration/TestData/SameFileFolders/TestComponents.wxs
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="utf-8"?>
+<Wix xmlns="http://wixtoolset.org/schemas/v4/wxs">
+  <Fragment>
+    <ComponentGroup Id="ProductComponents">
+      <Component  Directory="INSTALLFOLDER:\a">
+        <File Source="a\test.txt" />
+      </Component>
+      <Component  Directory="INSTALLFOLDER:\b">
+        <File Source="b\test.txt" />
+      </Component>
+      <Component  Directory="INSTALLFOLDER:\c">
+        <File Source="c\test.txt" />
+      </Component>
+    </ComponentGroup>
+  </Fragment>
+</Wix>
diff --git a/src/test/WixToolsetTest.CoreIntegration/TestData/SameFileFolders/data/a/test.txt b/src/test/WixToolsetTest.CoreIntegration/TestData/SameFileFolders/data/a/test.txt
new file mode 100644
index 00000000..1970cae6
--- /dev/null
+++ b/src/test/WixToolsetTest.CoreIntegration/TestData/SameFileFolders/data/a/test.txt
@@ -0,0 +1 @@
+This is a\test.txt.
\ No newline at end of file
diff --git a/src/test/WixToolsetTest.CoreIntegration/TestData/SameFileFolders/data/b/test.txt b/src/test/WixToolsetTest.CoreIntegration/TestData/SameFileFolders/data/b/test.txt
new file mode 100644
index 00000000..fa2c7082
--- /dev/null
+++ b/src/test/WixToolsetTest.CoreIntegration/TestData/SameFileFolders/data/b/test.txt
@@ -0,0 +1 @@
+This is b\test.txt.
\ No newline at end of file
diff --git a/src/test/WixToolsetTest.CoreIntegration/TestData/SameFileFolders/data/c/test.txt b/src/test/WixToolsetTest.CoreIntegration/TestData/SameFileFolders/data/c/test.txt
new file mode 100644
index 00000000..1c0cbda6
--- /dev/null
+++ b/src/test/WixToolsetTest.CoreIntegration/TestData/SameFileFolders/data/c/test.txt
@@ -0,0 +1 @@
+This is c\test.txt.
\ No newline at end of file
diff --git a/src/test/WixToolsetTest.CoreIntegration/WixToolsetTest.CoreIntegration.csproj b/src/test/WixToolsetTest.CoreIntegration/WixToolsetTest.CoreIntegration.csproj
index 1f8860ef..dba30bd6 100644
--- a/src/test/WixToolsetTest.CoreIntegration/WixToolsetTest.CoreIntegration.csproj
+++ b/src/test/WixToolsetTest.CoreIntegration/WixToolsetTest.CoreIntegration.csproj
@@ -36,6 +36,10 @@
     <Content Include="TestData\Font\FontTitle.wxs" CopyToOutputDirectory="PreserveNewest" />
     <Content Include="TestData\Icon\SampleIcon.wxs" CopyToOutputDirectory="PreserveNewest" />
     <Content Include="TestData\LockPermissions\EmptyPermissions.wxs" CopyToOutputDirectory="PreserveNewest" />
+    <Content Include="TestData\SameFileFolders\data\a\test.txt" CopyToOutputDirectory="PreserveNewest" />
+    <Content Include="TestData\SameFileFolders\data\c\test.txt" CopyToOutputDirectory="PreserveNewest" />
+    <Content Include="TestData\SameFileFolders\data\b\test.txt" CopyToOutputDirectory="PreserveNewest" />
+    <Content Include="TestData\SameFileFolders\TestComponents.wxs" CopyToOutputDirectory="PreserveNewest" />
     <Content Include="TestData\ProductWithComponentGroupRef\MinimalComponentGroup.wxs" CopyToOutputDirectory="PreserveNewest" />
     <Content Include="TestData\ProductWithComponentGroupRef\Product.wxs" CopyToOutputDirectory="PreserveNewest" />
     <Content Include="TestData\Registry\RegistryValue.wxs" CopyToOutputDirectory="PreserveNewest" />
diff --git a/src/test/WixToolsetTest.CoreIntegration/WixiplFixture.cs b/src/test/WixToolsetTest.CoreIntegration/WixiplFixture.cs
index 668c273a..1d359241 100644
--- a/src/test/WixToolsetTest.CoreIntegration/WixiplFixture.cs
+++ b/src/test/WixToolsetTest.CoreIntegration/WixiplFixture.cs
@@ -128,14 +128,14 @@ namespace WixToolsetTest.CoreIntegration
                 {
                     var binary = section.Tuples.OfType<BinaryTuple>().Single();
                     var path = binary[BinaryTupleFields.Data].AsPath().Path;
-                    Assert.Contains("Example.Extension", path);
-                    Assert.EndsWith(@"\0", path);
+                    Assert.StartsWith(Path.Combine(baseFolder, @"obj\Example.Extension"), path);
+                    Assert.EndsWith(@"wix-ir\example.txt", path);
                     Assert.Equal(@"BinFromWir", binary.Id.Id);
                 }
             }
         }
 
-        [Fact(Skip = "Test demonstrates failure")]
+        [Fact]
         public void CanBuildWixiplUsingExtensionLibrary()
         {
             var folder = TestData.Get(@"TestData\Wixipl");
@@ -171,7 +171,7 @@ namespace WixToolsetTest.CoreIntegration
 
                 result.AssertSuccess();
 
-                var intermediate = Intermediate.Load(Path.Combine(baseFolder, @"obj\test.wir"));
+                var intermediate = Intermediate.Load(Path.Combine(baseFolder, @"bin\test.wixpdb"));
                 var section = intermediate.Sections.Single();
 
                 {
@@ -183,8 +183,8 @@ namespace WixToolsetTest.CoreIntegration
                 {
                     var binary = section.Tuples.OfType<BinaryTuple>().Single();
                     var path = binary[BinaryTupleFields.Data].AsPath().Path;
-                    Assert.Contains("Example.Extension", path);
-                    Assert.EndsWith(@"\0", path);
+                    Assert.StartsWith(Path.Combine(baseFolder, @"obj\test"), path);
+                    Assert.EndsWith(@"wix-ir\example.txt", path);
                     Assert.Equal(@"BinFromWir", binary.Id.Id);
                 }
             }