Deps.json should include project references that aren't present in project.assets.json

src/Assets/TestProjects/AppWithTransitiveNonSdkProjectRefs/AuxLibrary/AuxLibrary.csproj

@@ -0,0 +1,58 @@
+<?xml version="1.0" encoding="utf-8"?>
+<Project ToolsVersion="14.0" DefaultTargets="Build" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
+  <Import Project="$(MSBuildExtensionsPath)\$(MSBuildToolsVersion)\Microsoft.Common.props" Condition="Exists('$(MSBuildExtensionsPath)\$(MSBuildToolsVersion)\Microsoft.Common.props')" />
+  <PropertyGroup>
+    <Configuration Condition=" '$(Configuration)' == '' ">Debug</Configuration>
+    <Platform Condition=" '$(Platform)' == '' ">AnyCPU</Platform>
+    <ProjectGuid>9a8d9cf9-379b-45c1-a95a-482ecb76a56c</ProjectGuid>
+    <OutputType>Library</OutputType>
+    <AppDesignerFolder>Properties</AppDesignerFolder>
+    <RootNamespace>$(MSBuildProjectName)</RootNamespace>
+    <AssemblyName>$(MSBuildProjectName)</AssemblyName>
+    <TargetFrameworkVersion>v4.6.2</TargetFrameworkVersion>
+    <FileAlignment>512</FileAlignment>
+    <AutoGenerateBindingRedirects>true</AutoGenerateBindingRedirects>
+  </PropertyGroup>
+  <PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Debug|AnyCPU' ">
+    <DebugSymbols>true</DebugSymbols>
+    <DebugType>full</DebugType>
+    <Optimize>false</Optimize>
+    <OutputPath>bin\Debug\</OutputPath>
+    <DefineConstants>DEBUG;TRACE</DefineConstants>
+    <ErrorReport>prompt</ErrorReport>
+    <WarningLevel>4</WarningLevel>
+  </PropertyGroup>
+  <PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Release|AnyCPU' ">
+    <DebugType>pdbonly</DebugType>
+    <Optimize>true</Optimize>
+    <OutputPath>bin\Release\</OutputPath>
+    <DefineConstants>TRACE</DefineConstants>
+    <ErrorReport>prompt</ErrorReport>
+    <WarningLevel>4</WarningLevel>
+  </PropertyGroup>
+  <ItemGroup>
+    <Reference Include="System"/>
+    <Reference Include="System.Core"/>
+    <Reference Include="System.Xml.Linq"/>
+    <Reference Include="System.Data.DataSetExtensions"/>
+    <Reference Include="Microsoft.CSharp"/>
+    <Reference Include="System.Data"/>
+    <Reference Include="System.Net.Http"/>
+    <Reference Include="System.Xml"/>
+  </ItemGroup>
+  <ItemGroup>
+    <Compile Include="**\*.cs" />
+  </ItemGroup>
+  <ItemGroup>
+    <PackageReference Include="Microsoft.NETFramework.ReferenceAssemblies" />
+  </ItemGroup>
+  <Import Project="$(MSBuildToolsPath)\Microsoft.CSharp.targets" />
+  <!-- To modify your build process, add your task inside one of the targets below and uncomment it. 
+       Other similar extension points exist, see Microsoft.Common.targets.
+  <Target Name="BeforeBuild">
+  </Target>
+  <Target Name="AfterBuild">
+  </Target>
+  -->
+
+ </Project>

src/Assets/TestProjects/AppWithTransitiveNonSdkProjectRefs/AuxLibrary/Helper.cs

@@ -0,0 +1,15 @@
+// Copyright (c) .NET Foundation and contributors. All rights reserved.
+// Licensed under the MIT license. See LICENSE file in the project root for full license information.
+
+using System;
+
+namespace AuxLibrary
+{
+    public static class Helper
+    {
+        public static void WriteMessage()
+        {
+            Console.WriteLine("This string came from AuxLibrary!");
+        }
+    }
+}

src/Assets/TestProjects/AppWithTransitiveNonSdkProjectRefs/MainLibrary/Helper.cs

@@ -0,0 +1,16 @@
+// Copyright (c) .NET Foundation and contributors. All rights reserved.
+// Licensed under the MIT license. See LICENSE file in the project root for full license information.
+
+using System;
+
+namespace MainLibrary
+{
+    public static class Helper
+    {
+        public static void WriteMessage()
+        {
+            Console.WriteLine("This string came from MainLibrary!");
+            AuxLibrary.Helper.WriteMessage();
+        }
+    }
+}

src/Assets/TestProjects/AppWithTransitiveNonSdkProjectRefs/MainLibrary/MainLibrary.csproj

@@ -0,0 +1,61 @@
+<?xml version="1.0" encoding="utf-8"?>
+<Project ToolsVersion="14.0" DefaultTargets="Build" xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
+  <Import Project="$(MSBuildExtensionsPath)\$(MSBuildToolsVersion)\Microsoft.Common.props" Condition="Exists('$(MSBuildExtensionsPath)\$(MSBuildToolsVersion)\Microsoft.Common.props')" />
+  <PropertyGroup>
+    <Configuration Condition=" '$(Configuration)' == '' ">Debug</Configuration>
+    <Platform Condition=" '$(Platform)' == '' ">AnyCPU</Platform>
+    <ProjectGuid>a60a2336-1e2d-4c7a-85cb-a9e890e2558b</ProjectGuid>
+    <OutputType>Library</OutputType>
+    <AppDesignerFolder>Properties</AppDesignerFolder>
+    <RootNamespace>$(MSBuildProjectName)</RootNamespace>
+    <AssemblyName>$(MSBuildProjectName)</AssemblyName>
+    <TargetFrameworkVersion>v4.6.2</TargetFrameworkVersion>
+    <FileAlignment>512</FileAlignment>
+    <AutoGenerateBindingRedirects>true</AutoGenerateBindingRedirects>
+  </PropertyGroup>
+  <PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Debug|AnyCPU' ">
+    <DebugSymbols>true</DebugSymbols>
+    <DebugType>full</DebugType>
+    <Optimize>false</Optimize>
+    <OutputPath>bin\Debug\</OutputPath>
+    <DefineConstants>DEBUG;TRACE</DefineConstants>
+    <ErrorReport>prompt</ErrorReport>
+    <WarningLevel>4</WarningLevel>
+  </PropertyGroup>
+  <PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Release|AnyCPU' ">
+    <DebugType>pdbonly</DebugType>
+    <Optimize>true</Optimize>
+    <OutputPath>bin\Release\</OutputPath>
+    <DefineConstants>TRACE</DefineConstants>
+    <ErrorReport>prompt</ErrorReport>
+    <WarningLevel>4</WarningLevel>
+  </PropertyGroup>
+  <ItemGroup>
+    <Reference Include="System"/>
+    <Reference Include="System.Core"/>
+    <Reference Include="System.Xml.Linq"/>
+    <Reference Include="System.Data.DataSetExtensions"/>
+    <Reference Include="Microsoft.CSharp"/>
+    <Reference Include="System.Data"/>
+    <Reference Include="System.Net.Http"/>
+    <Reference Include="System.Xml"/>
+  </ItemGroup>
+  <ItemGroup>
+    <ProjectReference Include="..\AuxLibrary\AuxLibrary.csproj" />
+  </ItemGroup>
+  <ItemGroup>
+    <Compile Include="**\*.cs" />
+  </ItemGroup>
+  <ItemGroup>
+    <PackageReference Include="Microsoft.NETFramework.ReferenceAssemblies" />
+  </ItemGroup>
+  <Import Project="$(MSBuildToolsPath)\Microsoft.CSharp.targets" />
+  <!-- To modify your build process, add your task inside one of the targets below and uncomment it. 
+       Other similar extension points exist, see Microsoft.Common.targets.
+  <Target Name="BeforeBuild">
+  </Target>
+  <Target Name="AfterBuild">
+  </Target>
+  -->
+
+ </Project>

src/Assets/TestProjects/AppWithTransitiveNonSdkProjectRefs/TestApp/Program.cs

@@ -0,0 +1,16 @@
+// Copyright (c) .NET Foundation and contributors. All rights reserved.
+// Licensed under the MIT license. See LICENSE file in the project root for full license information.
+
+using System;
+
+namespace TestApp
+{
+    public class Program
+    {
+        public static void Main(string[] args)
+        {
+            Console.WriteLine("TestApp --depends on--> MainLibrary --depends on--> AuxLibrary");
+            MainLibrary.Helper.WriteMessage();
+        }
+    }
+}

src/Assets/TestProjects/AppWithTransitiveNonSdkProjectRefs/TestApp/TestApp.csproj

@@ -0,0 +1,10 @@
+<Project Sdk="Microsoft.NET.Sdk">
+  <PropertyGroup>
+    <OutputType>Exe</OutputType>
+    <TargetFramework>$(CurrentTargetFramework)</TargetFramework>
+    <ProduceReferenceAssembly>false</ProduceReferenceAssembly>
+  </PropertyGroup>
+  <ItemGroup>
+    <ProjectReference Include="..\MainLibrary\MainLibrary.csproj" />
+  </ItemGroup>
+</Project>

src/Tasks/Microsoft.NET.Build.Tasks.UnitTests/GivenADependencyContextBuilder.cs

@@ -40,6 +40,7 @@ public void ItBuildsDependencyContextsFromProjectLockFiles(
             object[] resolvedNuGetFiles)
         {
             LockFile lockFile = TestLockFiles.GetLockFile(mainProjectName);
+            LockFileLookup lockFileLookup = new LockFileLookup(lockFile);
 
             SingleProjectInfo mainProject = SingleProjectInfo.Create(
                 "/usr/Path",
@@ -52,7 +53,7 @@ public void ItBuildsDependencyContextsFromProjectLockFiles(
                 ReferenceInfo.CreateDirectReferenceInfos(
                     referencePaths ?? new ITaskItem[] { },
                     referenceSatellitePaths ?? new ITaskItem[] { },
-                    projectContextHasProjectReferences: false,
+                    lockFileLookup: lockFileLookup,
                     i => true);
 
             ProjectContext projectContext = lockFile.CreateProjectContext(
@@ -67,7 +68,7 @@ public void ItBuildsDependencyContextsFromProjectLockFiles(
                 resolvedNuGetFiles = Array.Empty<ResolvedFile>();
             }
 
-            DependencyContext dependencyContext = new DependencyContextBuilder(mainProject, includeRuntimeFileVersions: false, runtimeGraph: null, projectContext: projectContext)
+            DependencyContext dependencyContext = new DependencyContextBuilder(mainProject, includeRuntimeFileVersions: false, runtimeGraph: null, projectContext: projectContext, libraryLookup: lockFileLookup)
                 .WithDirectReferences(directReferences)
                 .WithCompilationOptions(compilationOptions)
                 .WithResolvedNuGetFiles((ResolvedFile[]) resolvedNuGetFiles)
@@ -264,7 +265,7 @@ private DependencyContext BuildDependencyContextWithReferenceAssemblies(bool use
                 useCompilationOptions ? CreateCompilationOptions() :
                 null;
 
-            DependencyContext dependencyContext = new DependencyContextBuilder(mainProject, includeRuntimeFileVersions: false, runtimeGraph: null, projectContext: projectContext)
+            DependencyContext dependencyContext = new DependencyContextBuilder(mainProject, includeRuntimeFileVersions: false, runtimeGraph: null, projectContext: projectContext, libraryLookup: new LockFileLookup(lockFile))
                 .WithReferenceAssemblies(ReferenceInfo.CreateReferenceInfos(referencePaths))
                 .WithCompilationOptions(compilationOptions)
                 .Build();
@@ -325,7 +326,7 @@ public void ItCanGenerateTheRuntimeFallbackGraph()
             void CheckRuntimeFallbacks(string runtimeIdentifier, int fallbackCount)
             {
                 projectContext.LockFileTarget.RuntimeIdentifier = runtimeIdentifier;
-                var dependencyContextBuilder = new DependencyContextBuilder(mainProject, includeRuntimeFileVersions: false, runtimeGraph, projectContext);
+                var dependencyContextBuilder = new DependencyContextBuilder(mainProject, includeRuntimeFileVersions: false, runtimeGraph, projectContext, libraryLookup: new LockFileLookup(lockFile));
                 var runtimeFallbacks = dependencyContextBuilder.Build().RuntimeGraph;
 
                 runtimeFallbacks

src/Tasks/Microsoft.NET.Build.Tasks/DependencyContextBuilder.cs

@@ -47,14 +47,12 @@ internal class DependencyContextBuilder
 
         private const string NetCorePlatformLibrary = "Microsoft.NETCore.App";
 
-        public DependencyContextBuilder(SingleProjectInfo mainProjectInfo, bool includeRuntimeFileVersions, RuntimeGraph runtimeGraph, ProjectContext projectContext)
+        public DependencyContextBuilder(SingleProjectInfo mainProjectInfo, bool includeRuntimeFileVersions, RuntimeGraph runtimeGraph, ProjectContext projectContext, LockFileLookup libraryLookup)
         {
             _mainProjectInfo = mainProjectInfo;
             _includeRuntimeFileVersions = includeRuntimeFileVersions;
             _runtimeGraph = runtimeGraph;
 
-            var libraryLookup = new LockFileLookup(projectContext.LockFile);
-
             _dependencyLibraries = projectContext.LockFileTarget.Libraries
                 .Select(lockFileTargetLibrary =>
                 {

src/Tasks/Microsoft.NET.Build.Tasks/GenerateDepsFile.cs

@@ -125,20 +125,19 @@ private Dictionary<PackageIdentity, string> GetFilteredPackages()
 
         private void WriteDepsFile(string depsFilePath)
         {
-            ProjectContext projectContext;
-            if (AssetsFilePath == null)
-            {
-                projectContext = null;
-            }
-            else
+            ProjectContext projectContext = null;
+            LockFileLookup lockFileLookup = null;
+            if (AssetsFilePath != null)
             {
                 LockFile lockFile = new LockFileCache(this).GetLockFile(AssetsFilePath);
                 projectContext = lockFile.CreateProjectContext(
-                 TargetFramework,
-                 RuntimeIdentifier,
-                 PlatformLibraryName,
-                 RuntimeFrameworks,
-                 IsSelfContained);
+                    TargetFramework,
+                    RuntimeIdentifier,
+                    PlatformLibraryName,
+                    RuntimeFrameworks,
+                    IsSelfContained);
+
+                lockFileLookup = new LockFileLookup(lockFile);
             }
 
             CompilationOptions compilationOptions = CompilationOptionsConverter.ConvertFrom(CompilerOptions);
@@ -156,13 +155,14 @@ private void WriteDepsFile(string depsFilePath)
             IEnumerable<ReferenceInfo> referenceAssemblyInfos =
                 ReferenceInfo.CreateReferenceInfos(ReferenceAssemblies);
 
-            // If there is a generated asset file. The projectContext will have project reference.
-            // So remove it from directReferences to avoid duplication
-            var projectContextHasProjectReferences = projectContext != null;
+            // If there is a generated asset file. The projectContext will have most project references.
+            // So remove any project reference contained within projectContext from directReferences to avoid duplication
             IEnumerable<ReferenceInfo> directReferences =
-                ReferenceInfo.CreateDirectReferenceInfos(ReferencePaths,
+                ReferenceInfo.CreateDirectReferenceInfos(
+                    ReferencePaths,
                     ReferenceSatellitePaths,
-                    projectContextHasProjectReferences, isUserRuntimeAssembly);
+                    lockFileLookup,
+                    isUserRuntimeAssembly);
 
             IEnumerable<ReferenceInfo> dependencyReferences =
                 ReferenceInfo.CreateDependencyReferenceInfos(ReferenceDependencyPaths, ReferenceSatellitePaths, isUserRuntimeAssembly);
@@ -210,7 +210,7 @@ bool ShouldIncludeRuntimeAsset(ITaskItem item)
                 RuntimeGraph runtimeGraph =
                     IsSelfContained ? new RuntimeGraphCache(this).GetRuntimeGraph(RuntimeGraphPath) : null;
 
-                builder = new DependencyContextBuilder(mainProject, IncludeRuntimeFileVersions, runtimeGraph, projectContext);
+                builder = new DependencyContextBuilder(mainProject, IncludeRuntimeFileVersions, runtimeGraph, projectContext, lockFileLookup);
             }
             else
             {

src/Tasks/Microsoft.NET.Build.Tasks/ReferenceInfo.cs

@@ -54,17 +54,33 @@ public static IEnumerable<ReferenceInfo> CreateReferenceInfos(IEnumerable<ITaskI
         public static IEnumerable<ReferenceInfo> CreateDirectReferenceInfos(
             IEnumerable<ITaskItem> referencePaths,
             IEnumerable<ITaskItem> referenceSatellitePaths,
-            bool projectContextHasProjectReferences,
+            LockFileLookup lockFileLookup,
             Func<ITaskItem, bool> isRuntimeAssembly)
         {
-
-            bool filterOutProjectReferenceIfInProjectContextAlready(ITaskItem referencePath)
+            bool lockFileContainsProject(ITaskItem referencePath)
             {
-                return (projectContextHasProjectReferences ? !IsProjectReference(referencePath) : true);
+                if (lockFileLookup == null)
+                {
+                    return false;
+                }
+
+                if (!IsProjectReference(referencePath))
+                {
+                    return false;
+                }
+
+                string outputName = Path.GetFileName(referencePath.ItemSpec);
+                string projectName = Path.GetFileNameWithoutExtension(outputName);
+                if (string.IsNullOrEmpty(projectName))
+                {
+                    return true;
+                }
+
+                return lockFileLookup.GetProject(projectName) != null;
             }
 
             IEnumerable<ITaskItem> directReferencePaths = referencePaths
-                .Where(r => filterOutProjectReferenceIfInProjectContextAlready(r) && !IsNuGetReference(r) && isRuntimeAssembly(r));
+                .Where(r => !lockFileContainsProject(r) && !IsNuGetReference(r) && isRuntimeAssembly(r));
 
             return CreateFilteredReferenceInfos(directReferencePaths, referenceSatellitePaths);
         }
@@ -147,7 +163,7 @@ private static string GetVersion(ITaskItem referencePath)
                 if (!string.IsNullOrEmpty(fusionName))
                 {
                     AssemblyName assemblyName = new AssemblyName(fusionName);
-                    version = assemblyName.Version.ToString();
+                    version = assemblyName.Version?.ToString();
                 }
 
                 if (string.IsNullOrEmpty(version))