Subdirectory PBXGroup is also added to the main group, so Xcode 27.2 cannot open the project

Summary

When a target source resolves to the spec's own directory, XcodeGen can add a subdirectory PBXGroup to both its parent source group and the main group. This commonly occurs when project.yml is inside the module directory and uses sources: [../Module].

xcodegen generate exits successfully and prints no warning.

The same malformed structure was reported only as a warning in Xcode 10 (#405). Xcode 27.2 rejects it and cannot open the generated project. Its hierarchical project format does not allow a group to be a child of multiple groups.

Reproduction

Module/
├── project.yml
├── Extension/
│   └── a.swift
└── b.swift

Module/project.yml:

name: Module

targets:
  Module:
    type: framework
    platform: iOS
    sources:
      - ../Module

cd Module
xcodegen generate
xcodebuild -list -project Module.xcodeproj

Actual behavior

The generated project.pbxproj references the same Extension group from both Module and the main group:

0FFF97BD... /* Module */ = {
    isa = PBXGroup;
    children = (
        46BFE1FF... /* b.swift */,
        13188FF9... /* Extension */,
    );
    name = Module;
    path = .;
    sourceTree = "<group>";
};
AEF60E6A... /* main group */ = {
    isa = PBXGroup;
    children = (
        13188FF9... /* Extension */,
        0FFF97BD... /* Module */,
        ...
    );
    sourceTree = "<group>";
};

Xcode 27.2 fails to load the project:

xcodebuild: error: Unable to read project 'Module.xcodeproj'.
Reason: Could not open “Module”

The “PBXGroup” with ID “AEF60E6A...” has an invalid value for “children”.
The reference "Extension" is a member of more than one group, which is not allowed.

Expected behavior

Each PBXGroup should be a child of at most one group, and the generated project should open successfully in Xcode 27.2.

Environment

• XcodeGen: master
• Xcode 27.2 beta (27B5019j): fails to open the project
• Xcode 27.0: opens the same project and keeps one membership

Reproduce the issue from the described Module/project.yml using xcodegen generate, then inspect the generated Module.xcodeproj/project.pbxproj and its PBXGroup memberships. The work is done when each group has at most one parent and xcodebuild -list -project Module.xcodeproj opens successfully under Xcode 27.2.