Keep file elements in a single parent group

`getGroup` infers "top level" from the shape of the path, which stops
holding once the same directory is also reached as a child. Drop anything
that gets attached to a group from `rootGroups`, and rewrite its path,
project relative until now, to be relative to the new parent.

The TestProject fixture loses the duplicate `Folder` entry in the main group.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>

Author: Ckitakishi

Sources/XcodeGenKit/SourceGenerator.swift

@@ -335,6 +335,9 @@ class SourceGenerator {
     private func getGroup(path: Path, name: String? = nil, mergingChildren children: [PBXFileElement], createIntermediateGroups: Bool, hasCustomParent: Bool, isBaseGroup: Bool) -> PBXGroup {
         let groupReference: PBXGroup
 
+        // A child may already have been registered as top level before being attached to its parent.
+        removeRootGroupMembership(from: children)
+
         if let cachedGroup = groupsByPath[path] {
             var cachedGroupChildren = cachedGroup.children
             for child in children {
@@ -382,6 +385,19 @@ class SourceGenerator {
         return groupReference
     }
 
+    private func removeRootGroupMembership(from elements: [PBXFileElement]) {
+        for element in elements where rootGroups.contains(element) {
+            rootGroups.remove(element)
+            // Top-level group paths are relative to the project; nested group paths are relative to their parent.
+            guard element is PBXGroup, element.sourceTree == .group, let elementPath = element.path else { continue }
+            let relativePath = Path(elementPath).lastComponent
+            element.path = relativePath
+            if element.name == relativePath {
+                element.name = nil
+            }
+        }
+    }
+
     /// Creates a variant group or returns an existing one at the path
     private func getVariantGroup(path: Path, inPath: Path) -> PBXVariantGroup {
         let variantGroup: PBXVariantGroup

Tests/Fixtures/TestProject/Project.xcodeproj/project.pbxproj

@@ -1090,7 +1090,6 @@
 				4C7F5EB7D6F3E0E9B426AB4A /* Utilities */,
 				3FEA12CF227D41EF50E5C2DB /* Vendor */,
 				80C3A0E524EC1ABCB9149EA2 /* XPC Service */,
-				DAA7880242A9DE61E68026CC /* Folder */,
 				2E1E747C7BC434ADB80CC269 /* Headers */,
 				6B1603BA83AA0C7B94E45168 /* ResourceFolder */,
 				6BBE762F36D94AB6FFBFE834 /* SomeFile */,