Improve position warning context

[giovanni-br]

Fixes #2159.

This PR makes the set_and_check_new_positions warning easier to understand.

Previously, the warning only showed global atom indices, for example
mapping 0 : 4. This made it difficult to identify the affected atoms in a
real system.

The warning now includes the old and new residue names, residue IDs, chain IDs,
and atom names, while keeping the global atom indices for debugging.

Example:

mapping old atom 0 (residue LIG 1, chain X, atom C1x) to new atom 4
(residue LIG 2, chain 1, atom C2x) deviates by more than 1.0

Tested with:

python -m pytest -s --log-cli-level=WARNING \
  src/openfe/tests/protocols/openmm_rfe/test_hybrid_top_protocol.py::test_setup_ligand_overlap_warning

LLM / AI generated code disclosure

LLMs or other AI-powered tools (beyond simple IDE use cases) were used in this contribution: yes

Codex assisted with drafting the implementation and test update. I reviewed the
changes and ran the targeted test locally.

Checklist

• All new code is appropriately documented.
• Added a news entry, or the changes are not user-facing.
• Ran pre-commit.
• Filled in the AI generated code disclosure.

Manual Tests: not run; this change only improves warning messages.

• GPU integration tests
• example notebook testing
• packaging tests

Developers certificate of origin

• I certify that this contribution is covered by the MIT License and the Developer Certificate of Origin.

[giovanni-br]

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