Fix TargetSource group behavior

When targeting a file, a folder should not be created for its directory,
only the file should appear in the specified custom group.
Moreover, if the custom groups contains actual filesystem folders, they
should map to these.

Sources/XcodeGenKit/SourceGenerator.swift

@@ -281,6 +281,7 @@ class SourceGenerator {
                 // Check equality by path and sourceTree because XcodeProj.PBXObject.== is very slow.
                 if !cachedGroupChildren.contains(where: { $0.name == child.name && $0.path == child.path && $0.sourceTree == child.sourceTree }) {
                     cachedGroupChildren.append(child)
+                    child.parent = cachedGroup
                 }
             }
             cachedGroup.children = cachedGroupChildren
@@ -394,7 +395,6 @@ class SourceGenerator {
         targetSource: TargetSource,
         path: Path,
         isBaseGroup: Bool,
-        createIntermediateGroups: Bool,
         hasCustomParent: Bool,
         excludePaths: Set<Path>,
         includePaths: Set<Path>
@@ -426,7 +426,6 @@ class SourceGenerator {
                 targetSource: targetSource,
                 path: path,
                 isBaseGroup: false,
-                createIntermediateGroups: createIntermediateGroups,
                 hasCustomParent: false,
                 excludePaths: excludePaths,
                 includePaths: includePaths
@@ -581,7 +580,10 @@ class SourceGenerator {
 
             let sourceFile = generateSourceFile(targetType: targetType, targetSource: targetSource, path: path)
 
-            if parentPath == project.basePath {
+            if hasCustomParent {
+                sourcePath = path
+                sourceReference = fileReference
+            } else if parentPath == project.basePath {
                 sourcePath = path
                 sourceReference = fileReference
                 rootGroups.insert(fileReference)
@@ -609,7 +611,6 @@ class SourceGenerator {
                 targetSource: targetSource,
                 path: path,
                 isBaseGroup: true,
-                createIntermediateGroups: createIntermediateGroups,
                 hasCustomParent: hasCustomParent,
                 excludePaths: excludePaths,
                 includePaths: includePaths
@@ -626,6 +627,7 @@ class SourceGenerator {
 
         if hasCustomParent {
             createParentGroups(customParentGroups, for: sourceReference)
+            try makePathRelative(for: sourceReference, at: path)
         } else if createIntermediateGroups {
             createIntermediaGroups(for: sourceReference, at: sourcePath)
         }
@@ -639,21 +641,24 @@ class SourceGenerator {
         }
 
         let parentPath = project.basePath + Path(parentGroups.joined(separator: "/"))
+        let parentPathExists = parentPath.exists
+        let parentGroupAlreadyExists = groupsByPath[parentPath] != nil
 
-        let hasParentGroup = groupsByPath[parentPath] != nil
         let parentGroup = getGroup(
             path: parentPath,
             mergingChildren: [fileElement],
             createIntermediateGroups: false,
             hasCustomParent: false,
-            isBaseGroup: false
+            isBaseGroup: parentGroups.count == 1
         )
 
         // As this path is a custom group, remove the path reference
-        parentGroup.name = String(parentName)
-        parentGroup.path = nil
+        if !parentPathExists {
+            parentGroup.name = String(parentName)
+            parentGroup.path = nil
+        }
 
-        if !hasParentGroup {
+        if !parentGroupAlreadyExists {
             createParentGroups(parentGroups.dropLast(), for: parentGroup)
         }
     }
@@ -681,6 +686,32 @@ class SourceGenerator {
         }
     }
 
+    // Make the fileElement path and name relative to its parents aggregated paths
+    private func makePathRelative(for fileElement: PBXFileElement, at path: Path) throws {
+        // This makes the fileElement path relative to its parent and not to the project. Xcode then rebuilds the actual
+        // path for the file based on the hierarchy this fileElement lives in.
+        var paths: [String] = []
+        var element: PBXFileElement = fileElement
+        while true {
+            guard let parent = element.parent else { break }
+
+            if let path = parent.path {
+                paths.insert(path, at: 0)
+            }
+
+            element = parent
+        }
+
+        let completePath = project.basePath + Path(paths.joined(separator: "/"))
+        let relativePath = try path.relativePath(from: completePath)
+        let relativePathString = relativePath.string
+
+        if relativePathString != fileElement.path {
+            fileElement.path = relativePathString
+            fileElement.name = relativePath.lastComponent
+        }
+    }
+
     private func findCurrentCoreDataModelVersionPath(using versionedModels: [Path]) -> Path? {
         // Find and parse the current version model stored in the .xccurrentversion file
         guard