Fix folder source path regression with createIntermediateGroups (#1603)

[yonaskolb]

Summary

• Fixes type: folder source generates incorrect PBXFileReference path in 2.45.0 #1603 where type: folder sources generated a PBXFileReference with only the leaf directory name instead of the full relative path when createIntermediateGroups was enabled
• PR Various synced folder enhancements #1596 added makePathRelative to the createIntermediateGroups code path for synced folders, but it inadvertently also ran for regular .folder sources which use sourceTree: .sourceRoot and need the full path preserved
• Skips makePathRelative for .folder type sources; .syncedFolder and other types are unaffected

Test plan

• Added test case "generates folder references with createIntermediateGroups"
• Existing folder reference test still passes
• Full test suite passes (74 tests, 0 failures)

🤖 Generated with Claude Code

[Lutzifer]

thx for the fix, it came faster than I could create an issue for it