Only adding rids for full framework TFMs if the project.json does not already have Runtimes in its Runtimes section.

TestAssets/TestProjects/TestAppWithMultipleFrameworksAndRuntimes/Program.cs

@@ -0,0 +1,17 @@
+using System;
+using System.Xml;
+
+namespace ConsoleApplication
+{
+    public class Program
+    {
+        public static void Main()
+        {
+            Console.WriteLine("Hello World!");
+#if NET20 || NET35 || NET45 || NET461
+            // Force XmlDocument to be used
+            var doc = new XmlDocument();
+#endif
+        }
+    }
+}

TestAssets/TestProjects/TestAppWithMultipleFrameworksAndRuntimes/project.json

@@ -0,0 +1,38 @@
+{
+  "version": "1.0.0-*",
+  "buildOptions": {
+    "emitEntryPoint": true
+  },
+  "dependencies": {},
+  "frameworks": {
+    "net20": {
+      "frameworkAssemblies": {
+        "System.Xml": {}
+      }
+    },
+    "net35": {
+      "frameworkAssemblies": {
+        "System.Xml": {}
+      }
+    },
+    "net40": {
+      "frameworkAssemblies": {
+        "System.Xml": {}
+      }
+    },
+    "net461": {
+      "frameworkAssemblies": {
+        "System.Xml": {}
+      }
+    },
+    "netcoreapp1.0": {
+      "dependencies": {
+        "Microsoft.NetCore.App": "1.0.1"
+      }
+    }
+  },
+  "runtimes": {
+    "win7-x64": {},
+    "win7-x86": {}
+  }
+}

src/Microsoft.DotNet.ProjectJsonMigration/Rules/MigrateTFMRule.cs

@@ -6,6 +6,7 @@ using System.Globalization;
 using System.Linq;
 using System.Text;
 using Microsoft.Build.Construction;
+using Microsoft.DotNet.Internal.ProjectModel;
 using Microsoft.DotNet.ProjectJsonMigration.Transforms;
 using NuGet.Frameworks;
 using System.Collections.Generic;
@@ -42,7 +43,7 @@ namespace Microsoft.DotNet.ProjectJsonMigration.Rules
                     mergeExisting: true);
                 _transformApplicator.Execute(
                     FrameworkRuntimeIdentifiersTransform.Transform(
-                        migrationRuleInputs.ProjectContexts.Single().TargetFramework),
+                        migrationRuleInputs.ProjectContexts.Single()),
                     propertyGroup,
                     mergeExisting: true);
             }
@@ -53,9 +54,14 @@ namespace Microsoft.DotNet.ProjectJsonMigration.Rules
                         migrationRuleInputs.ProjectContexts.Select(p => p.TargetFramework)),
                     propertyGroup,
                     mergeExisting: true);
+
+
+                var runtimes = string.Join(",", migrationRuleInputs.ProjectContexts.Select(p => p.RuntimeIdentifier));
+                Console.WriteLine($"Runtimes = {runtimes}");
+
                 _transformApplicator.Execute(
                     FrameworksRuntimeIdentifiersTransform.Transform(
-                        migrationRuleInputs.ProjectContexts.Select(p => p.TargetFramework)),
+                        migrationRuleInputs.ProjectContexts),
                     propertyGroup,
                     mergeExisting: true);
             }
@@ -122,11 +128,12 @@ namespace Microsoft.DotNet.ProjectJsonMigration.Rules
                 frameworks => string.Join(";", frameworks.Select(f => f.GetShortFolderName())),
                 frameworks => true);
 
-        private AddPropertyTransform<IEnumerable<NuGetFramework>> FrameworksRuntimeIdentifiersTransform =>
+        private AddPropertyTransform<IEnumerable<ProjectContext>> FrameworksRuntimeIdentifiersTransform =>
-            new AddPropertyTransform<IEnumerable<NuGetFramework>>(
+            new AddPropertyTransform<IEnumerable<ProjectContext>>(
                 "RuntimeIdentifiers",
-                frameworks => RuntimeIdentifiers,
+                projectContexts => RuntimeIdentifiers,
-                frameworks => frameworks.Any(f => !f.IsPackageBased));
+                projectContexts => projectContexts.All(p => !p.ProjectFile.Runtimes.Any()) &&
+                                   projectContexts.Any(p => !p.TargetFramework.IsPackageBased));
 
         private AddPropertyTransform<NuGetFramework> FrameworkTransform =>
             new AddPropertyTransform<NuGetFramework>(
@@ -134,10 +141,11 @@ namespace Microsoft.DotNet.ProjectJsonMigration.Rules
                 framework => framework.GetShortFolderName(),
                 framework => true);
 
-        private AddPropertyTransform<NuGetFramework> FrameworkRuntimeIdentifiersTransform =>
+        private AddPropertyTransform<ProjectContext> FrameworkRuntimeIdentifiersTransform =>
-            new AddPropertyTransform<NuGetFramework>(
+            new AddPropertyTransform<ProjectContext>(
                 "RuntimeIdentifiers",
-                framework => RuntimeIdentifiers,
+                projectContext => RuntimeIdentifiers,
-                framework => !framework.IsPackageBased);
+                projectContext => !projectContext.ProjectFile.Runtimes.Any() &&
+                                  !projectContext.TargetFramework.IsPackageBased);
     }
 }

test/Microsoft.DotNet.ProjectJsonMigration.Tests/Rules/GivenThatIWantToMigrateTFMs.cs

@@ -16,7 +16,7 @@ namespace Microsoft.DotNet.ProjectJsonMigration.Tests
     public class GivenThatIWantToMigrateTFMs : TestBase
     {
         [Fact(Skip="Emitting this until x-targetting full support is in")]
-        public void Migrating_netcoreapp_project_Does_not_populate_TargetFrameworkIdentifier_and_TargetFrameworkVersion()
+        public void MigratingNetcoreappProjectDoesNotPopulateTargetFrameworkIdentifierAndTargetFrameworkVersion()
         {
             var testDirectory = Temp.CreateDirectory().Path;
             var testPJ = new ProjectJsonBuilder(TestAssetsManager)
@@ -44,7 +44,7 @@ namespace Microsoft.DotNet.ProjectJsonMigration.Tests
         }
 
         [Fact]
-        public void Migrating_MultiTFM_project_Populates_TargetFrameworks_with_short_tfms()
+        public void MigratingMultiTFMProjectPopulatesTargetFrameworksWithShortTfms()
         {
             var testDirectory = Temp.CreateDirectory().Path;
             var testPJ = new ProjectJsonBuilder(TestAssetsManager)
@@ -69,7 +69,7 @@ namespace Microsoft.DotNet.ProjectJsonMigration.Tests
         }
 
         [Fact]
-        public void Migrating_desktop_TFMs_adds_RuntimeIdentifiers()
+        public void MigratingDesktopTFMsAddsAllRuntimeIdentifiersIfTheProjectDoesNothaveAnyAlready()
         {
             var testDirectory = Temp.CreateDirectory().Path;
             var testPJ = new ProjectJsonBuilder(TestAssetsManager)
@@ -94,7 +94,31 @@ namespace Microsoft.DotNet.ProjectJsonMigration.Tests
         }
 
         [Fact]
-        public void Migrating_Single_TFM_project_Populates_TargetFramework()
+        public void MigrateTFMRuleDoesNotAddRuntimesWhenMigratingDesktopTFMsWithRuntimesAlready()
+        {
+            var testDirectory = Temp.CreateDirectory().Path;
+            var testPJ = new ProjectJsonBuilder(TestAssetsManager)
+                .FromTestAssetBase("TestAppWithMultipleFrameworksAndRuntimes")
+                .SaveToDisk(testDirectory);
+
+            var projectContexts = ProjectContext.CreateContextForEachFramework(testDirectory);
+            var mockProj = ProjectRootElement.Create();
+
+            var migrationSettings =
+                MigrationSettings.CreateMigrationSettingsTestHook(testDirectory, testDirectory, mockProj);
+            var migrationInputs = new MigrationRuleInputs(
+                projectContexts, 
+                mockProj, 
+                mockProj.AddItemGroup(), 
+                mockProj.AddPropertyGroup());
+
+            new MigrateTFMRule().Apply(migrationSettings, migrationInputs);
+
+            mockProj.Properties.Count(p => p.Name == "RuntimeIdentifiers").Should().Be(0);
+        }
+
+        [Fact]
+        public void MigratingSingleTFMProjectPopulatesTargetFramework()
         {
             var testDirectory = Temp.CreateDirectory().Path;
             var testPJ = new ProjectJsonBuilder(TestAssetsManager)