Fix composite ReadyToRun publish when RelativePath has a path component

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

@@ -202,6 +202,13 @@ private void ProcessInputFileList(
                     }
                 }
 
+                // The on-disk path of the R2R output that will be copied to the publish directory.
+                // For separately compiled images this matches the '--out' path passed to crossgen2 (which honors any
+                // subdirectory in RelativePath). For component assemblies of a composite image, crossgen2 emits them
+                // flat into the composite output directory using only their file names, so the publish source path must
+                // use just the file name while RelativePath continues to drive the final publish destination.
+                var outputR2RImagePublishPath = outputR2RImage;
+
                 if (eligibility.CompileSeparately)
                 {
                     // This TaskItem is the IL->R2R entry, for an input assembly that needs to be compiled into a R2R image. This will be used as
@@ -219,17 +226,19 @@ private void ProcessInputFileList(
                 else if (eligibility.CompileUnrootedIntoCompositeImage)
                 {
                     r2rCompositeUnrootedInput.Add(file);
+                    outputR2RImagePublishPath = Path.Combine(OutputPath, Path.GetFileName(outputR2RImageRelativePath));
                 }
                 else if (eligibility.CompileIntoCompositeImage)
                 {
                     r2rCompositeInputList.Add(file);
+                    outputR2RImagePublishPath = Path.Combine(OutputPath, Path.GetFileName(outputR2RImageRelativePath));
                 }
 
                 // This TaskItem corresponds to the output R2R image. It is equivalent to the input TaskItem, only the ItemSpec for it points to the new path
                 // for the newly created R2R image
                 TaskItem r2rFileToPublish = new(file)
                 {
-                    ItemSpec = outputR2RImage
+                    ItemSpec = outputR2RImagePublishPath
                 };
                 r2rFileToPublish.RemoveMetadata(MetadataKeys.OriginalItemSpec);
                 r2rFilesPublishList.Add(r2rFileToPublish);

test/Microsoft.NET.Publish.Tests/GivenThatWeWantToPublishReadyToRun.cs

@@ -230,6 +230,59 @@ void It_can_publish_readytorun_using_crossgen2_composite_mode(string targetFrame
             TestProjectPublishing_Internal("Crossgen2TestApp", targetFramework, isSelfContained: true, emitNativeSymbols: false, useCrossgen2: true, composite: true, identifier: targetFramework);
         }
 
+        [RequiresMSBuildVersionTheory("17.0.0.32901")]
+        [InlineData(ToolsetInfo.CurrentTargetFramework)]
+        void It_can_publish_readytorun_composite_with_subdirectory_relative_path(string targetFramework)
+        {
+            // Regression test for https://github.com/dotnet/runtime/issues/79902
+            // When a target rewrites the RelativePath of the published assemblies to include a subdirectory,
+            // composite ReadyToRun publishing used to fail because the SDK looked for the crossgen2 component
+            // output under that subdirectory even though crossgen2 emits the components flat into the composite
+            // output directory.
+            var projectName = "Crossgen2SubdirApp";
+
+            var testProject = CreateTestProjectForR2RTesting(
+                targetFramework,
+                projectName,
+                "ClassLib");
+
+            testProject.AdditionalProperties["PublishReadyToRun"] = "True";
+            testProject.AdditionalProperties["PublishReadyToRunUseCrossgen2"] = "True";
+            testProject.AdditionalProperties["PublishReadyToRunComposite"] = "True";
+            testProject.SelfContained = "True";
+
+            var testProjectInstance = _testAssetsManager.CreateTestProject(testProject, identifier: targetFramework)
+                .WithProjectChanges(project =>
+                {
+                    var ns = project.Root.Name.Namespace;
+                    var target = new XElement(ns + "Target",
+                        new XAttribute("Name", "PublishAssembliesToSubdirectory"),
+                        new XAttribute("BeforeTargets", "CreateReadyToRunImages"),
+                        new XAttribute("AfterTargets", "ComputeResolvedFilesToPublishList"),
+                        new XElement(ns + "ItemGroup",
+                            new XElement(ns + "ResolvedFileToPublish",
+                                new XAttribute("Update", "@(ResolvedFileToPublish)"),
+                                new XAttribute("Condition", "'%(Extension)' == '.dll'"),
+                                new XAttribute("RelativePath", "subdir/%(RelativePath)"))));
+                    project.Root.Add(target);
+                });
+
+            var publishCommand = new PublishCommand(testProjectInstance);
+            publishCommand.Execute().Should().Pass();
+
+            DirectoryInfo publishDirectory = publishCommand.GetOutputDirectory(
+                targetFramework,
+                "Debug",
+                testProject.RuntimeIdentifier);
+
+            var subdirectory = new DirectoryInfo(Path.Combine(publishDirectory.FullName, "subdir"));
+            subdirectory.Should().HaveFile($"{projectName}.dll");
+            subdirectory.Should().HaveFile("ClassLib.dll");
+
+            DoesImageHaveR2RInfo(Path.Combine(subdirectory.FullName, $"{projectName}.dll")).Should().BeTrue();
+            DoesImageHaveR2RInfo(Path.Combine(subdirectory.FullName, "ClassLib.dll")).Should().BeTrue();
+        }
+
         [RequiresMSBuildVersionTheory("17.0.0.32901")]
         [InlineData("net6.0")]
         [InlineData(ToolsetInfo.CurrentTargetFramework)]