Fix makePathRelative using wrong base path when projectDirectory differs (#1606)

`makePathRelative` used `project.basePath` to compute parent paths, while
`resolveGroupPath` used `projectDirectory ?? project.basePath`. When these
differ (e.g. via --project flag), intermediate group paths become inconsistent,
causing Xcode to resolve files to the wrong location.

Regression from #1596 which added the `makePathRelative` call in the
`createIntermediateGroups` code path.

Co-Authored-By: Claude Opus 4.6 <[email protected]>

Author: yonaskolb

Sources/XcodeGenKit/SourceGenerator.swift

@@ -886,7 +886,7 @@ class SourceGenerator {
             element = parent
         }
 
-        let completePath = project.basePath + Path(paths.joined(separator: "/"))
+        let completePath = (projectDirectory ?? project.basePath) + Path(paths.joined(separator: "/"))
         let relativePath = try path.relativePath(from: completePath)
         let relativePathString = relativePath.string
 

Tests/XcodeGenKitTests/SourceGeneratorTests.swift

@@ -911,6 +911,40 @@ class SourceGeneratorTests: XCTestCase {
                 try pbxProj.expectFile(paths: ["Sources/B", "b.swift"], names: ["B", "b.swift"], buildPhase: .sources)
             }
 
+            $0.it("generates intermediate groups with different projectDirectory") {
+
+                let directories = """
+                Sources:
+                  - a.swift
+                  - b.swift
+                Modules:
+                  - m.swift
+                """
+                try createDirectories(directories)
+
+                let target = Target(name: "Test", type: .application, platform: .iOS, sources: [
+                    "../Sources",
+                    "../Modules",
+                ])
+                let options = SpecOptions(createIntermediateGroups: true)
+                // basePath is a subdirectory (simulating spec in a subdir like ProjectRoot/XcodeGen/)
+                // projectDirectory is the parent (simulating --project pointing to ProjectRoot/)
+                let subdir = directoryPath + "SubDir"
+                try subdir.mkpath()
+                let project = Project(basePath: subdir, name: "Test", targets: [target], options: options)
+
+                let generator = PBXProjGenerator(project: project, projectDirectory: directoryPath)
+                let pbxProj = try generator.generate()
+
+                // Sources and Modules should have path = "Sources"/"Modules" (not "../Sources")
+                // The intermediate group for TestDirectory should have path = "."
+                // So Xcode resolves: projectDir/./Sources = correct
+                // Before fix: path was "../Sources", resolving to projectDir/./../Sources = wrong
+                try pbxProj.expectFile(paths: [".", "Sources", "a.swift"], names: ["TestDirectory", "Sources", "a.swift"], buildPhase: .sources)
+                try pbxProj.expectFile(paths: [".", "Sources", "b.swift"], names: ["TestDirectory", "Sources", "b.swift"], buildPhase: .sources)
+                try pbxProj.expectFile(paths: [".", "Modules", "m.swift"], names: ["TestDirectory", "Modules", "m.swift"], buildPhase: .sources)
+            }
+
             $0.it("generates custom groups") {
 
                 let directories = """