diff --git a/scripts/dotnet-cli-build/CompileTargets.cs b/scripts/dotnet-cli-build/CompileTargets.cs
index 17056f0f8..60136fe78 100644
--- a/scripts/dotnet-cli-build/CompileTargets.cs
+++ b/scripts/dotnet-cli-build/CompileTargets.cs
@@ -18,7 +18,6 @@ namespace Microsoft.DotNet.Cli.Build
     public class CompileTargets
     {
         public static readonly string CoreCLRVersion = "1.0.2-rc2-24008";
-        public static readonly string AppDepSdkVersion = "1.0.6-prerelease-00003";
         public static readonly bool IsWinx86 = CurrentPlatform.IsWindows && CurrentArchitecture.Isx86;
 
         public static readonly string[] BinariesForCoreHost = new[]
@@ -49,9 +48,9 @@ namespace Microsoft.DotNet.Cli.Build
             return c.Success();
         }
 
-        // Moving PrepareTargets.RestorePackages after PackagePkgProjects because managed code depends on the 
+        // Moving PrepareTargets.RestorePackages after PackagePkgProjects because managed code depends on the
         // Microsoft.NETCore.App package that is created during PackagePkgProjects.
-        [Target(nameof(PrepareTargets.Init), nameof(PackagePkgProjects), nameof(PrepareTargets.RestorePackages), nameof(CompileStage1), nameof(CompileStage2))]
+        [Target(nameof(PrepareTargets.Init), nameof(CompileCoreHost), nameof(PackagePkgProjects), nameof(PrepareTargets.RestorePackages), nameof(CompileStage1), nameof(CompileStage2))]
         public static BuildTargetResult Compile(BuildTargetContext c)
         {
             return c.Success();
@@ -145,7 +144,7 @@ namespace Microsoft.DotNet.Cli.Build
             return c.Success();
         }
 
-        [Target(nameof(CompileCoreHost))]
+        [Target]
         public static BuildTargetResult PackagePkgProjects(BuildTargetContext c)
         {
             var buildVersion = c.BuildContext.Get<BuildVersion>("BuildVersion");
@@ -231,7 +230,6 @@ namespace Microsoft.DotNet.Cli.Build
         public static BuildTargetResult CompileStage1(BuildTargetContext c)
         {
             CleanBinObj(c, Path.Combine(c.BuildContext.BuildDirectory, "src"));
-            CleanBinObj(c, Path.Combine(c.BuildContext.BuildDirectory, "test"));
 
             if (Directory.Exists(Dirs.Stage1))
             {
@@ -259,7 +257,6 @@ namespace Microsoft.DotNet.Cli.Build
             var configuration = c.BuildContext.Get<string>("Configuration");
 
             CleanBinObj(c, Path.Combine(c.BuildContext.BuildDirectory, "src"));
-            CleanBinObj(c, Path.Combine(c.BuildContext.BuildDirectory, "test"));
 
             if (Directory.Exists(Dirs.Stage2))
             {
@@ -533,13 +530,6 @@ namespace Microsoft.DotNet.Cli.Build
             File.Delete(compilersDeps);
             File.Delete(compilersRuntimeConfig);
 
-            // Copy AppDeps
-            var result = CopyAppDeps(c, outputDir);
-            if (!result.Success)
-            {
-                return result;
-            }
-
             // Generate .version file
             var version = buildVersion.NuGetVersion;
             var content = $@"{c.BuildContext["CommitHash"]}{Environment.NewLine}{version}{Environment.NewLine}";
@@ -548,53 +538,6 @@ namespace Microsoft.DotNet.Cli.Build
             return c.Success();
         }
 
-        private static BuildTargetResult CopyAppDeps(BuildTargetContext c, string outputDir)
-        {
-            var appDepOutputDir = Path.Combine(outputDir, "appdepsdk");
-            Rmdir(appDepOutputDir);
-            Mkdirp(appDepOutputDir);
-
-            // Find toolchain package
-            string packageId;
-
-            if (CurrentPlatform.IsWindows)
-            {
-                if (CurrentArchitecture.Isx86)
-                {
-                    // https://github.com/dotnet/cli/issues/1550
-                    c.Warn("Native compilation is not yet working on Windows x86");
-                    return c.Success();
-                }
-
-                packageId = "toolchain.win7-x64.Microsoft.DotNet.AppDep";
-            }
-            else if (CurrentPlatform.IsUbuntu)
-            {
-                packageId = "toolchain.ubuntu.14.04-x64.Microsoft.DotNet.AppDep";
-            }
-            else if (CurrentPlatform.IsCentOS || CurrentPlatform.IsRHEL || CurrentPlatform.IsDebian)
-            {
-                c.Warn($"Native compilation is not yet working on {CurrentPlatform.Current}");
-                return c.Success();
-            }
-            else if (CurrentPlatform.IsOSX)
-            {
-                packageId = "toolchain.osx.10.10-x64.Microsoft.DotNet.AppDep";
-            }
-            else
-            {
-                return c.Failed("Unsupported OS Platform");
-            }
-
-            var appDepPath = Path.Combine(
-                Dirs.NuGetPackages,
-                packageId,
-                AppDepSdkVersion);
-            CopyRecursive(appDepPath, appDepOutputDir, overwrite: true);
-
-            return c.Success();
-        }
-
         public static BuildTargetResult CrossgenSharedFx(BuildTargetContext c, string pathToAssemblies)
         {
             // Check if we need to skip crossgen
@@ -620,7 +563,7 @@ namespace Microsoft.DotNet.Cli.Build
                 // in CompileTargets and the one in the shared library project.json match and are updated in lock step, but long term
                 // we need to be able to look at the project.lock.json file and figure out what version of Microsoft.NETCore.Runtime.CoreCLR
                 // was used, and then select that version.
-                ExecSilent(Crossgen.GetCrossgenPathForVersion(CompileTargets.CoreCLRVersion),
+                ExecSilent(Crossgen.GetCrossgenPathForVersion(CoreCLRVersion),
                     "-readytorun", "-in", file, "-out", tempPathName, "-platform_assemblies_paths", pathToAssemblies);
 
                 File.Delete(file);
diff --git a/scripts/dotnet-cli-build/PrepareTargets.cs b/scripts/dotnet-cli-build/PrepareTargets.cs
index 56c06a8e6..ce65668ad 100644
--- a/scripts/dotnet-cli-build/PrepareTargets.cs
+++ b/scripts/dotnet-cli-build/PrepareTargets.cs
@@ -228,7 +228,7 @@ namespace Microsoft.DotNet.Cli.Build
         {
             var dotnet = DotNetCli.Stage0;
 
-            dotnet.Restore("--verbosity", "verbose", "--disable-parallel", "--infer-runtimes", "--fallbacksource", Dirs.Corehost)
+            dotnet.Restore("--verbosity", "verbose", "--disable-parallel", "--fallbacksource", Dirs.Corehost)
                 .WorkingDirectory(Path.Combine(c.BuildContext.BuildDirectory, "src"))
                 .Execute()
                 .EnsureSuccessful();
diff --git a/scripts/update-dependencies/project.json b/scripts/update-dependencies/project.json
index caf880730..4d0144085 100644
--- a/scripts/update-dependencies/project.json
+++ b/scripts/update-dependencies/project.json
@@ -9,7 +9,7 @@
     "Microsoft.CSharp": "4.0.1-rc2-24008",
     "System.Runtime.Serialization.Primitives": "4.1.1-rc2-24008",
     "Microsoft.DotNet.Cli.Build.Framework": "1.0.0-*",
-    "NuGet.Versioning": "3.5.0-beta-1130",
+    "NuGet.Versioning": "3.5.0-beta-1160",
     "Newtonsoft.Json": "7.0.1",
     "Octokit": "0.18.0",
     "Microsoft.Net.Http": "2.2.29"
diff --git a/src/Microsoft.DotNet.Cli.Utils/CommandResolution/ProjectToolsCommandResolver.cs b/src/Microsoft.DotNet.Cli.Utils/CommandResolution/ProjectToolsCommandResolver.cs
index 49514db98..374d48b51 100644
--- a/src/Microsoft.DotNet.Cli.Utils/CommandResolution/ProjectToolsCommandResolver.cs
+++ b/src/Microsoft.DotNet.Cli.Utils/CommandResolution/ProjectToolsCommandResolver.cs
@@ -19,7 +19,7 @@ namespace Microsoft.DotNet.Cli.Utils
 {
     public class ProjectToolsCommandResolver : ICommandResolver
     {
-        private static readonly NuGetFramework s_toolPackageFramework = FrameworkConstants.CommonFrameworks.NetStandardApp15;
+        private static readonly NuGetFramework s_toolPackageFramework = FrameworkConstants.CommonFrameworks.NetCoreApp10;
         
         private static readonly CommandResolutionStrategy s_commandResolutionStrategy = 
             CommandResolutionStrategy.ProjectToolsPackage;
diff --git a/src/Microsoft.DotNet.Cli.Utils/project.json b/src/Microsoft.DotNet.Cli.Utils/project.json
index 795108289..28c970794 100644
--- a/src/Microsoft.DotNet.Cli.Utils/project.json
+++ b/src/Microsoft.DotNet.Cli.Utils/project.json
@@ -7,10 +7,10 @@
   "dependencies": {
     "Microsoft.DotNet.ProjectModel": "1.0.0-*",
     "Microsoft.Extensions.PlatformAbstractions": "1.0.0-rc2-20459",
-    "NuGet.Versioning": "3.5.0-beta-1130",
-    "NuGet.Packaging": "3.5.0-beta-1130",
-    "NuGet.Frameworks": "3.5.0-beta-1130",
-    "NuGet.ProjectModel": "3.5.0-beta-1130"
+    "NuGet.Versioning": "3.5.0-beta-1160",
+    "NuGet.Packaging": "3.5.0-beta-1160",
+    "NuGet.Frameworks": "3.5.0-beta-1160",
+    "NuGet.ProjectModel": "3.5.0-beta-1160"
   },
   "frameworks": {
     "net451": {
@@ -22,8 +22,7 @@
     },
     "netstandard1.5": {
       "imports": [
-        "portable-net45+wp80+win8+wpa81+dnxcore50",
-        "dnxcore50"
+        "portable-net45+wp80+win8+wpa81+dnxcore50"
       ],
       "dependencies": {
         "System.Diagnostics.Process": "4.1.0-rc2-24008"
diff --git a/src/Microsoft.DotNet.Compiler.Common/project.json b/src/Microsoft.DotNet.Compiler.Common/project.json
index 403a4ba60..5d64a9153 100644
--- a/src/Microsoft.DotNet.Compiler.Common/project.json
+++ b/src/Microsoft.DotNet.Compiler.Common/project.json
@@ -13,8 +13,7 @@
   "frameworks": {
     "netstandard1.5": {
       "imports": [
-        "portable-net45+wp80+win8+wpa81+dnxcore50",
-        "dnxcore50"
+        "portable-net45+wp80+win8+wpa81+dnxcore50"
       ]
     }
   },
diff --git a/src/Microsoft.DotNet.Files/project.json b/src/Microsoft.DotNet.Files/project.json
index 33a563790..103d989d1 100644
--- a/src/Microsoft.DotNet.Files/project.json
+++ b/src/Microsoft.DotNet.Files/project.json
@@ -12,8 +12,7 @@
   "frameworks": {
     "netstandard1.5": {
       "imports": [
-        "portable-net45+wp80+win8+wpa81+dnxcore50",
-        "dnxcore50"
+        "portable-net45+wp80+win8+wpa81+dnxcore50"
       ]
     }
   },
diff --git a/src/Microsoft.DotNet.ProjectModel.Workspaces/project.json b/src/Microsoft.DotNet.ProjectModel.Workspaces/project.json
index 74b6335ee..fd711f0eb 100644
--- a/src/Microsoft.DotNet.ProjectModel.Workspaces/project.json
+++ b/src/Microsoft.DotNet.ProjectModel.Workspaces/project.json
@@ -12,8 +12,7 @@
     "netstandard1.5": {
       "imports": [
         "portable-net45+wp80+win8+wpa81+dnxcore50",
-        "portable-net45+win8",
-        "dnxcore50"
+        "portable-net45+win8"
       ]
     }
   }
diff --git a/src/Microsoft.DotNet.ProjectModel/project.json b/src/Microsoft.DotNet.ProjectModel/project.json
index 321004869..787d638ae 100644
--- a/src/Microsoft.DotNet.ProjectModel/project.json
+++ b/src/Microsoft.DotNet.ProjectModel/project.json
@@ -16,8 +16,8 @@
       "version": "1.0.0-rc2-20221"
     },
     "Newtonsoft.Json": "7.0.1",
-    "NuGet.Packaging": "3.5.0-beta-1130",
-    "NuGet.RuntimeModel": "3.5.0-beta-1130",
+    "NuGet.Packaging": "3.5.0-beta-1160",
+    "NuGet.RuntimeModel": "3.5.0-beta-1160",
     "System.Reflection.Metadata": "1.3.0-rc2-24008"
   },
   "frameworks": {
diff --git a/src/Microsoft.DotNet.TestFramework/project.json b/src/Microsoft.DotNet.TestFramework/project.json
index 928b8102a..d6cb24b7f 100644
--- a/src/Microsoft.DotNet.TestFramework/project.json
+++ b/src/Microsoft.DotNet.TestFramework/project.json
@@ -12,8 +12,7 @@
   "frameworks": {
     "netstandard1.5": {
       "imports": [
-        "portable-net45+wp80+win8+wpa81+dnxcore50",
-        "dnxcore50"
+        "portable-net45+wp80+win8+wpa81+dnxcore50"
       ]
     }
   }
diff --git a/src/corehost/cli/fxr/fx_muxer.cpp b/src/corehost/cli/fxr/fx_muxer.cpp
index a9ebde2ed..f206922c9 100644
--- a/src/corehost/cli/fxr/fx_muxer.cpp
+++ b/src/corehost/cli/fxr/fx_muxer.cpp
@@ -292,7 +292,7 @@ int fx_muxer_t::parse_args_and_execute(
         }
 
         app_candidate = argv[cur_i];
-        bool is_app_runnable = ends_with(app_candidate, _X(".dll"), false) || ends_with(app_candidate, _X(".exe"), false);
+        bool is_app_runnable = (ends_with(app_candidate, _X(".dll"), false) || ends_with(app_candidate, _X(".exe"), false)) && pal::realpath(&app_candidate);
         trace::verbose(_X("App %s runnable=[%d]"), app_candidate.c_str(), is_app_runnable);
         // If exec mode is on, then check we have a dll at this point
         if (exec_mode)
@@ -300,6 +300,7 @@ int fx_muxer_t::parse_args_and_execute(
             if (!is_app_runnable)
             {
                 trace::error(_X("dotnet exec needs a dll to execute. Try dotnet [--help]"));
+                *is_an_app = false;
                 return InvalidArgFailure;
             }
         }
diff --git a/src/dotnet/commands/dotnet-build/CompileContext.cs b/src/dotnet/commands/dotnet-build/CompileContext.cs
index 2a9ff80bc..7469d5e9e 100644
--- a/src/dotnet/commands/dotnet-build/CompileContext.cs
+++ b/src/dotnet/commands/dotnet-build/CompileContext.cs
@@ -12,6 +12,7 @@ using Microsoft.DotNet.ProjectModel;
 using Microsoft.DotNet.ProjectModel.Utilities;
 using Microsoft.DotNet.Tools.Compiler;
 using Microsoft.Extensions.PlatformAbstractions;
+using Microsoft.DotNet.ProjectModel.Compilation;
 
 namespace Microsoft.DotNet.Tools.Build
 {
@@ -79,7 +80,7 @@ namespace Microsoft.DotNet.Tools.Build
                 return true;
             }
 
-            foreach (var dependency in Sort(_rootProjectDependencies.ProjectDependenciesWithSources))
+            foreach (var dependency in Sort(_rootProjectDependencies))
             {
                 var dependencyProjectContext = ProjectContext.Create(dependency.Path, dependency.Framework, new[] { _rootProject.RuntimeIdentifier });
 
@@ -514,31 +515,40 @@ namespace Microsoft.DotNet.Tools.Build
             executable.MakeCompilationOutputRunnable();
         }
 
-        private static ISet<ProjectDescription> Sort(Dictionary<string, ProjectDescription> projects)
+        private static IEnumerable<ProjectDescription> Sort(ProjectDependenciesFacade dependencies)
         {
-            var outputs = new HashSet<ProjectDescription>();
+            var outputs = new List<ProjectDescription>();
 
-            foreach (var pair in projects)
+            foreach (var pair in dependencies.Dependencies)
             {
-                Sort(pair.Value, projects, outputs);
+                Sort(pair.Value, dependencies, outputs);
             }
 
-            return outputs;
+            return outputs.Distinct(new ProjectComparer());
         }
 
-        private static void Sort(ProjectDescription project, Dictionary<string, ProjectDescription> projects, ISet<ProjectDescription> outputs)
+        private static void Sort(LibraryExport node, ProjectDependenciesFacade dependencies, IList<ProjectDescription> outputs)
         {
             // Sorts projects in dependency order so that we only build them once per chain
-            foreach (var dependency in project.Dependencies)
+            ProjectDescription projectDependency;
+            foreach (var dependency in node.Library.Dependencies)
             {
-                ProjectDescription projectDependency;
-                if (projects.TryGetValue(dependency.Name, out projectDependency))
-                {
-                    Sort(projectDependency, projects, outputs);
-                }
+                // Sort the children
+                Sort(dependencies.Dependencies[dependency.Name], dependencies, outputs);
             }
 
-            outputs.Add(project);
+            // Add this node to the list if it is a project
+            if (dependencies.ProjectDependenciesWithSources.TryGetValue(node.Library.Identity.Name, out projectDependency))
+            {
+                // Add to the list of projects to build
+                outputs.Add(projectDependency);
+            }
+        }
+
+        private class ProjectComparer : IEqualityComparer<ProjectDescription>
+        {
+            public bool Equals(ProjectDescription x, ProjectDescription y) => string.Equals(x.Identity.Name, y.Identity.Name, StringComparison.Ordinal);
+            public int GetHashCode(ProjectDescription obj) => obj.Identity.Name.GetHashCode();
         }
 
         public struct CompilerIO
diff --git a/src/dotnet/commands/dotnet-build/ProjectDependenciesFacade.cs b/src/dotnet/commands/dotnet-build/ProjectDependenciesFacade.cs
index cc5086404..5d8f9372d 100644
--- a/src/dotnet/commands/dotnet-build/ProjectDependenciesFacade.cs
+++ b/src/dotnet/commands/dotnet-build/ProjectDependenciesFacade.cs
@@ -14,7 +14,7 @@ namespace Microsoft.DotNet.Tools.Build
     {
         // projectName -> ProjectDescription
         public Dictionary<string, ProjectDescription> ProjectDependenciesWithSources { get; }
-        public List<LibraryExport> Dependencies { get; }
+        public Dictionary<string, LibraryExport> Dependencies { get; }
 
         public ProjectDependenciesFacade(ProjectContext rootProject, string configValue)
         {
@@ -25,7 +25,7 @@ namespace Microsoft.DotNet.Tools.Build
             // Build project references
             foreach (var dependency in Dependencies)
             {
-                var projectDependency = dependency.Library as ProjectDescription;
+                var projectDependency = dependency.Value.Library as ProjectDescription;
 
                 if (projectDependency != null && projectDependency.Resolved && projectDependency.Project.Files.SourceFiles.Any())
                 {
@@ -35,7 +35,7 @@ namespace Microsoft.DotNet.Tools.Build
         }
 
         // todo make extension of ProjectContext?
-        private static List<LibraryExport> GetProjectDependencies(ProjectContext projectContext, string configuration)
+        private static Dictionary<string, LibraryExport> GetProjectDependencies(ProjectContext projectContext, string configuration)
         {
             // Create the library exporter
             var exporter = projectContext.CreateExporter(configuration);
@@ -43,7 +43,7 @@ namespace Microsoft.DotNet.Tools.Build
             // Gather exports for the project
             var dependencies = exporter.GetDependencies().ToList();
 
-            return dependencies;
+            return dependencies.ToDictionary(d => d.Library.Identity.Name);
         }
     }
 
diff --git a/src/dotnet/commands/dotnet-publish/PublishCommand.cs b/src/dotnet/commands/dotnet-publish/PublishCommand.cs
index 90ae4e8fb..f035550f2 100644
--- a/src/dotnet/commands/dotnet-publish/PublishCommand.cs
+++ b/src/dotnet/commands/dotnet-publish/PublishCommand.cs
@@ -1,21 +1,20 @@
 // 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 Microsoft.DotNet.Cli.Utils;
-using Microsoft.DotNet.ProjectModel;
-using Microsoft.DotNet.ProjectModel.Compilation;
-using NuGet.Frameworks;
 using System;
 using System.Collections.Generic;
 using System.IO;
 using System.Linq;
 using Microsoft.DotNet.Cli.Compiler.Common;
-using Microsoft.Extensions.PlatformAbstractions;
+using Microsoft.DotNet.Cli.Utils;
 using Microsoft.DotNet.Files;
-using Microsoft.DotNet.Tools.Common;
-using Microsoft.DotNet.ProjectModel.Utilities;
+using Microsoft.DotNet.ProjectModel;
+using Microsoft.DotNet.ProjectModel.Compilation;
 using Microsoft.DotNet.ProjectModel.Graph;
-using NuGet.Versioning;
+using Microsoft.DotNet.ProjectModel.Utilities;
+using Microsoft.DotNet.Tools.Common;
+using Microsoft.Extensions.PlatformAbstractions;
+using NuGet.Frameworks;
 
 namespace Microsoft.DotNet.Tools.Publish
 {
@@ -134,6 +133,10 @@ namespace Microsoft.DotNet.Tools.Publish
                 .ToDictionary(e => e.Library.Identity.Name);
             var collectExclusionList = context.IsPortable ? GetExclusionList(context, packageExports) : new HashSet<string>();
 
+            // Get the output paths used by the call to `dotnet build` above (since we didn't pass `--output`, they will be different from
+            // our current output paths)
+            var buildOutputPaths = context.GetOutputPaths(configuration, buildBasePath);
+
             var exports = exporter.GetAllExports();
             foreach (var export in exports.Where(e => !collectExclusionList.Contains(e.Library.Identity.Name)))
             {
@@ -141,6 +144,19 @@ namespace Microsoft.DotNet.Tools.Publish
 
                 PublishAssetGroups(export.RuntimeAssemblyGroups, outputPath, nativeSubdirectories: false, includeRuntimeGroups: context.IsPortable);
                 PublishAssetGroups(export.NativeLibraryGroups, outputPath, nativeSubdirectories, includeRuntimeGroups: context.IsPortable);
+
+                var runtimeAssetsToCopy = export.RuntimeAssets.Where(a => ShouldCopyExportRuntimeAsset(context, buildOutputPaths, export, a));
+                runtimeAssetsToCopy.StructuredCopyTo(outputPath, outputPaths.IntermediateOutputDirectoryPath);
+            }
+
+            if (context.ProjectFile.HasRuntimeOutput(configuration) && !context.TargetFramework.IsDesktop())
+            {
+                PublishFiles(
+                    new[] {
+                        buildOutputPaths.RuntimeFiles.DepsJson,
+                        buildOutputPaths.RuntimeFiles.RuntimeConfigJson
+                    },
+                    outputPath);
             }
 
             if (options.PreserveCompilationContext.GetValueOrDefault())
@@ -151,9 +167,6 @@ namespace Microsoft.DotNet.Tools.Publish
                 }
             }
 
-            var buildOutputPaths = context.GetOutputPaths(configuration, buildBasePath, null);
-            PublishBuildOutputFiles(buildOutputPaths, context, outputPath, Configuration);
-
             var contentFiles = new ContentFiles(context);
             contentFiles.StructuredCopyTo(outputPath);
 
@@ -171,59 +184,26 @@ namespace Microsoft.DotNet.Tools.Publish
             return true;
         }
 
-        private void PublishBuildOutputFiles(OutputPaths buildOutputPaths, ProjectContext context, string outputPath, string configuration)
+        /// <summary>
+        /// Filters which export's RuntimeAssets should get copied to the output path.
+        /// </summary>
+        /// <returns>
+        /// True if the asset should be copied to the output path; otherwise, false.
+        /// </returns>
+        private static bool ShouldCopyExportRuntimeAsset(ProjectContext context, OutputPaths buildOutputPaths, LibraryExport export, LibraryAsset asset)
         {
-            List<string> filesToPublish = new List<string>();
+            // The current project has the host .exe in its runtime assets, but it shouldn't be copied
+            // to the output path during publish. The host will come from the export that has the real host in it.
 
-            string[]  buildOutputFiles = null;
-
-            if (context.ProjectFile.HasRuntimeOutput(configuration))
+            if (context.RootProject.Identity == export.Library.Identity)
             {
-                Reporter.Verbose.WriteLine($"publish: using runtime build output files");
-
-                buildOutputFiles = new string[] 
+                if (asset.ResolvedPath == buildOutputPaths.RuntimeFiles.Executable)
                 {
-                    buildOutputPaths.RuntimeFiles.DepsJson,
-                    buildOutputPaths.RuntimeFiles.RuntimeConfigJson,
-                    buildOutputPaths.RuntimeFiles.Config,
-                    buildOutputPaths.RuntimeFiles.Assembly,
-                    buildOutputPaths.RuntimeFiles.PdbPath,
-                    Path.ChangeExtension(buildOutputPaths.RuntimeFiles.Assembly, "xml")
-                };
-
-                filesToPublish.AddRange(buildOutputPaths.RuntimeFiles.Resources());
-            }
-            else
-            {
-                Reporter.Verbose.WriteLine($"publish: using compilation build output files");
-
-                buildOutputFiles = new string[] 
-                {
-                    buildOutputPaths.CompilationFiles.Assembly,
-                    buildOutputPaths.CompilationFiles.PdbPath,
-                    Path.ChangeExtension(buildOutputPaths.CompilationFiles.Assembly, "xml")
-                };
-
-                filesToPublish.AddRange(buildOutputPaths.CompilationFiles.Resources());
-            }
-
-            foreach (var buildOutputFile in buildOutputFiles)
-            {
-                if (File.Exists(buildOutputFile))
-                {
-                    filesToPublish.Add(buildOutputFile);
-                }
-                else
-                {
-                    Reporter.Verbose.WriteLine($"publish: build output file not found {buildOutputFile} ");
+                    return false;
                 }
             }
-            
-            Reporter.Verbose.WriteLine($"publish: Copying build output files:\n {string.Join("\n", filesToPublish)}");
 
-            PublishFiles(
-                filesToPublish,
-                outputPath);
+            return true;
         }
 
         private bool InvokeBuildOnProject(ProjectContext context, string buildBasePath, string configuration)
diff --git a/src/dotnet/project.json b/src/dotnet/project.json
index e8baa2eec..e6bd4fb92 100644
--- a/src/dotnet/project.json
+++ b/src/dotnet/project.json
@@ -17,10 +17,10 @@
   ],
   "dependencies": {
     "NuGet.Commands": {
-      "version": "3.5.0-beta-1130",
+      "version": "3.5.0-beta-1160",
       "exclude": "compile"
     },
-    "NuGet.CommandLine.XPlat": "3.5.0-beta-1130",
+    "NuGet.CommandLine.XPlat": "3.5.0-beta-1160",
     "Newtonsoft.Json": "7.0.1",
     "System.Text.Encoding.CodePages": "4.0.1-rc2-24008",
     "System.Diagnostics.FileVersionInfo": "4.0.0-rc2-24008",
@@ -55,13 +55,13 @@
     }
   },
   "frameworks": {
-    "netstandard1.5": {
-      "imports": [
-        "dnxcore50",
-        "netstandardapp1.5",
-        "portable-net45+win8",
-        "portable-net45+wp80+win8+wpa81+dnxcore50"
-      ]
+    "netcoreapp1.0": {
+        "imports": [
+            "dnxcore50",
+            "netstandardapp1.5",
+            "portable-net45+win8",
+            "portable-net45+wp80+win8+wpa81+dnxcore50"
+        ]
     }
   }
 }
diff --git a/test/Microsoft.DotNet.Cli.Utils.Tests/GivenAProjectToolsCommandResolver.cs b/test/Microsoft.DotNet.Cli.Utils.Tests/GivenAProjectToolsCommandResolver.cs
index fee3a0417..a8889d522 100644
--- a/test/Microsoft.DotNet.Cli.Utils.Tests/GivenAProjectToolsCommandResolver.cs
+++ b/test/Microsoft.DotNet.Cli.Utils.Tests/GivenAProjectToolsCommandResolver.cs
@@ -28,7 +28,7 @@ namespace Microsoft.DotNet.Cli.Utils.Tests
 {
     public class GivenAProjectToolsCommandResolver
     {
-        private static readonly NuGetFramework s_toolPackageFramework = FrameworkConstants.CommonFrameworks.NetStandardApp15;
+        private static readonly NuGetFramework s_toolPackageFramework = FrameworkConstants.CommonFrameworks.NetCoreApp10;
 
         private static readonly string s_liveProjectDirectory = 
             Path.Combine(AppContext.BaseDirectory, "TestAssets/TestProjects/AppWithToolDependency");
diff --git a/test/Microsoft.DotNet.Cli.Utils.Tests/project.json b/test/Microsoft.DotNet.Cli.Utils.Tests/project.json
index 2f693bd56..37cb5ae94 100644
--- a/test/Microsoft.DotNet.Cli.Utils.Tests/project.json
+++ b/test/Microsoft.DotNet.Cli.Utils.Tests/project.json
@@ -10,10 +10,10 @@
     },
     "System.Diagnostics.TraceSource": "4.0.0-rc2-24008",
     "System.Runtime.Serialization.Primitives": "4.1.1-rc2-24008",
-    "NuGet.Versioning": "3.5.0-beta-1130",
-    "NuGet.Packaging": "3.5.0-beta-1130",
-    "NuGet.Frameworks": "3.5.0-beta-1130",
-    "NuGet.ProjectModel": "3.5.0-beta-1130",
+    "NuGet.Versioning": "3.5.0-beta-1160",
+    "NuGet.Packaging": "3.5.0-beta-1160",
+    "NuGet.Frameworks": "3.5.0-beta-1160",
+    "NuGet.ProjectModel": "3.5.0-beta-1160",
     "Microsoft.DotNet.ProjectModel": {
       "target": "project"
     },
diff --git a/test/dotnet-publish.Tests/PublishAppWithDependencies.cs b/test/dotnet-publish.Tests/PublishAppWithDependencies.cs
new file mode 100644
index 000000000..df2907f82
--- /dev/null
+++ b/test/dotnet-publish.Tests/PublishAppWithDependencies.cs
@@ -0,0 +1,46 @@
+// 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.IO;
+using Microsoft.DotNet.TestFramework;
+using Microsoft.DotNet.Tools.Test.Utilities;
+using Xunit;
+
+namespace Microsoft.DotNet.Tools.Publish.Tests
+{
+    public class PublishAppWithDependencies : TestBase
+    {
+        [Fact]
+        public void PublishTestAppWithContentPackage()
+        {
+            var testInstance = TestAssetsManager.CreateTestInstance("TestAppWithContentPackage")
+                .WithLockFiles();
+
+            var publishCommand = new PublishCommand(testInstance.TestRoot);
+            var publishResult = publishCommand.Execute();
+
+            publishResult.Should().Pass();
+
+            var publishDir = publishCommand.GetOutputDirectory(portable: false);
+
+            publishDir.Should().HaveFiles(new[]
+            {
+                $"AppWithContentPackage{publishCommand.GetExecutableExtension()}",
+                "AppWithContentPackage.dll",
+                "AppWithContentPackage.deps.json"
+            });
+
+            // these files come from the contentFiles of the SharedContentA dependency
+            publishDir
+                .Sub("scripts")
+                .Should()
+                .Exist()
+                .And
+                .HaveFile("run.cmd");
+
+            publishDir
+                .Should()
+                .HaveFile("config.xml");
+        }
+    }
+}
diff --git a/test/dotnet-test.Tests/GivenThatWeWantToRunTestsInTheConsole.cs b/test/dotnet-test.Tests/GivenThatWeWantToRunTestsInTheConsole.cs
index e431ca7ee..be0286aaf 100644
--- a/test/dotnet-test.Tests/GivenThatWeWantToRunTestsInTheConsole.cs
+++ b/test/dotnet-test.Tests/GivenThatWeWantToRunTestsInTheConsole.cs
@@ -21,7 +21,7 @@ namespace Microsoft.Dotnet.Tools.Test.Tests
         {
             var testAssetManager = new TestAssetsManager(Path.Combine(RepoRoot, "TestAssets"));
             var testInstance =
-                testAssetManager.CreateTestInstance("ProjectWithTests", identifier: "ConsoleTests").WithLockFiles();
+                testAssetManager.CreateTestInstance("ProjectWithTests", identifier: "ConsoleTests");
 
             _projectFilePath = Path.Combine(testInstance.TestRoot, "project.json");
             var contexts = ProjectContext.CreateContextForEachFramework(
@@ -29,6 +29,11 @@ namespace Microsoft.Dotnet.Tools.Test.Tests
                 null,
                 PlatformServices.Default.Runtime.GetAllCandidateRuntimeIdentifiers());
 
+            // Restore the project again in the destination to resolve projects
+            // Since the lock file has project relative paths in it, those will be broken
+            // unless we re-restore
+            new RestoreCommand() { WorkingDirectory = testInstance.TestRoot }.Execute().Should().Pass();
+
             _defaultOutputPath = Path.Combine(testInstance.TestRoot, "bin", "Debug", "netcoreapp1.0");
         }
 
diff --git a/test/dotnet-test.Tests/GivenThatWeWantToUseDotnetTestE2EInDesignTime.cs b/test/dotnet-test.Tests/GivenThatWeWantToUseDotnetTestE2EInDesignTime.cs
index a3e4fd1af..65ed16756 100644
--- a/test/dotnet-test.Tests/GivenThatWeWantToUseDotnetTestE2EInDesignTime.cs
+++ b/test/dotnet-test.Tests/GivenThatWeWantToUseDotnetTestE2EInDesignTime.cs
@@ -20,7 +20,7 @@ namespace Microsoft.Dotnet.Tools.Test.Tests
         public GivenThatWeWantToUseDotnetTestE2EInDesignTime()
         {
             var testAssetManager = new TestAssetsManager(Path.Combine(RepoRoot, "TestAssets"));
-            var testInstance = testAssetManager.CreateTestInstance("ProjectWithTests").WithLockFiles();
+            var testInstance = testAssetManager.CreateTestInstance("ProjectWithTests");
 
             _projectFilePath = Path.Combine(testInstance.TestRoot, "project.json");
             var contexts = ProjectContext.CreateContextForEachFramework(
@@ -28,6 +28,11 @@ namespace Microsoft.Dotnet.Tools.Test.Tests
                 null,
                 PlatformServices.Default.Runtime.GetAllCandidateRuntimeIdentifiers());
 
+            // Restore the project again in the destination to resolve projects
+            // Since the lock file has project relative paths in it, those will be broken
+            // unless we re-restore
+            new RestoreCommand() { WorkingDirectory = testInstance.TestRoot }.Execute().Should().Pass();
+
             _outputPath = Path.Combine(testInstance.TestRoot, "bin", "Debug", "netcoreapp1.0");
             var buildCommand = new BuildCommand(_projectFilePath);
             var result = buildCommand.Execute();
diff --git a/tools/RuntimeGraphGenerator/project.json b/tools/RuntimeGraphGenerator/project.json
index 12f43b9c6..efe35c501 100644
--- a/tools/RuntimeGraphGenerator/project.json
+++ b/tools/RuntimeGraphGenerator/project.json
@@ -4,8 +4,8 @@
     "emitEntryPoint": true
   },
   "dependencies": {
-    "NuGet.RuntimeModel": "3.5.0-beta-1130",
-    "NuGet.Versioning": "3.5.0-beta-1130",
+    "NuGet.RuntimeModel": "3.5.0-beta-1160",
+    "NuGet.Versioning": "3.5.0-beta-1160",
     "System.CommandLine": "0.1.0-e160119-1",
     "System.Runtime.Serialization.Json": "4.0.2-rc2-24008",
     "Microsoft.DotNet.ProjectModel": "1.0.0-*",
diff --git a/tools/appdep/project.json b/tools/appdep/project.json
deleted file mode 100644
index d0388306d..000000000
--- a/tools/appdep/project.json
+++ /dev/null
@@ -1,15 +0,0 @@
-{
-  "version": "1.0.0-*",
-  "compilationOptions": {
-    "emitEntryPoint": true
-  },
-  "dependencies": {
-    "NETStandard.Library": "1.5.0-rc2-24008",
-    "Microsoft.DotNet.AppDep": "1.0.6-prerelease-00003"
-  },
-  "frameworks": {
-    "netstandardapp1.5": {
-      "imports": "dnxcore50"
-    }
-  }
-}