Fix hang when createIntermediateGroups reaches the file system root

CHANGELOG.md

@@ -18,6 +18,7 @@
 - Fix nested target attributes (e.g. `attributes.SystemCapabilities`) being serialized as a stringified Swift `Dictionary` description instead of a proper nested plist dictionary, which also caused non-deterministic key ordering in generated `project.pbxproj` files across runs #1639 @imadaan @sergeyospanov
 - Fix `.DS_Store` and `.orig` files causing projects to be regenerated when using `--use-cache` #1622 @kimjune01
 - Fix generated "Copy Bundle Resources" phases missing `dstPath`, which caused Xcode 27.2 project conversion to fail #1654 @Ckitakishi
+- Fix `xcodegen generate` hanging when `createIntermediateGroups` is enabled and a source's only common ancestor with the project is the file system root, such as an absolute path like `/usr/bin/xcrun` #1659 @ybai08
 
 ### Internal
 - Use a dedicated local package in the SPM fixture so generated fixtures don't depend on the checkout directory name, such as when running tests from a git worktree @yonaskolb

Sources/XcodeGenKit/SourceGenerator.swift

@@ -856,8 +856,8 @@ class SourceGenerator {
     private func createIntermediaGroups(for fileElement: PBXFileElement, at path: Path) {
 
         let parentPath = path.parent()
-        guard parentPath != project.basePath else {
-            // we've reached the top
+        guard parentPath != project.basePath, parentPath != path else {
+            // we've reached the top, or the root of the file system
             return
         }
 

Tests/XcodeGenKitTests/SourceGeneratorTests.swift

@@ -961,6 +961,26 @@ class SourceGeneratorTests: XCTestCase {
                 try pbxProj.expectFile(paths: ["Sources/B", "b.swift"], names: ["B", "b.swift"], buildPhase: .sources)
             }
 
+            $0.it("generates intermediate groups up to the file system root") {
+                try createDirectories("""
+                Sources:
+                  - a.swift
+                """)
+
+                let target = Target(name: "Test", type: .application, platform: .iOS, sources: [
+                    "Sources",
+                    "/usr/bin/env",
+                ])
+                let options = SpecOptions(createIntermediateGroups: true)
+                let basePath = directoryPath.absolute()
+                let project = Project(basePath: basePath, name: "Test", targets: [target], options: options)
+
+                let pbxProj = try project.generatePbxProj()
+                let rootPath = try Path("/").relativePath(from: basePath).string
+                try pbxProj.expectFile(paths: ["Sources", "a.swift"], buildPhase: .sources)
+                try pbxProj.expectFile(paths: [rootPath, "usr", "bin", "env"], names: ["/", "usr", "bin", "env"])
+            }
+
             $0.it("generates intermediate groups with different projectDirectory") {
 
                 let directories = """