doc: Document build.commands working directory (#11218)

I just got bit by this trying to do
```yaml
build:
  commands:
    - cd docs
    - myst build --html
```

After the `cd docs`, the next command is reset to the main repo root

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- User's documentation (`docs`):
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Author: LecrisUT

docs/user/config-file/v2.rst

@@ -557,6 +557,11 @@ See :doc:`/build-customization` for more details.
 
    ``build.os`` and ``build.tools`` are also required when using ``build.commands``.
 
+.. note::
+
+   All items in the ``build.commands`` array are executed in a clean shell environment, i.e. environment changes do not
+   persist and the working directory always start from the git repo.
+
 :Type: ``list``
 :Required: ``false``
 :Default: ``[]``