[Bug]: Warning is issued when a document is added to multiple parents

Summary

Guides does not support adding a document to 2 different parents in the toctree. This is supported by Sphinx.

Although probably not relevant, the warnings that are issued create a lot of noise when building the Symfony docs: https://github.com/wouterj/symfony-docs-guides/actions/runs/19391242509/job/55484996045

Code snippet that reproduces the problem

Create a small doc with a toctree like this:

index.rst
├─ design.rst
├─ implementation.rst
│  ├─ design.rst
│  └─ test.rst
└─ release.rst

.. index.rst

Homepage
========

.. toctree::

    design
    implementation
    release

.. implementation.rst

Implementation
==============

.. toctree::

    design
    test

The design.rst now has both Index and Implementation as parents.
This triggers a warning with Guides:

app.WARNING: Document design has been added to parents index and implementation. The `toctree`
directive changes the position of documents in the document tree. Use the `menu` directive to
only display a menu without changing the document tree.

Expected output

Sphinx accepts the doc structure, and generates a toctree order like this:

1. index
2. design
3. implementation
4. test
5. release

Reproduce the warning with the shown index.rst, implementation.rst, design.rst, release.rst, and test.rst toctree structure, then trace where Guides reports multiple parents during the documentation build. Compare the resulting order and warnings with the expected Sphinx behavior; done means the valid shared document no longer produces this warning and the expected toctree order is preserved.