fix: isolate Zeo++ output runs

[tdpham2]

Summary

• Create a unique persistent child directory for every legacy Zeo++ invocation and expose the actual artifact path in the result.
• Reject mixed-stem Zeo++ output directories so analyses from unrelated structures cannot be combined.
• Include artifact directories in batch records and document deferred review findings 2-7.

Compatibility

• An explicit output_dir is now a parent directory; callers receive the concrete run directory in result["output_dir"].
• Temporary runs still clean up automatically and return no persistent output directory.
• Existing result fields and direct-file/single-stem parsing remain available.

Testing

• PYTHONPATH=src pytest -q tests/test_zeopp.py tests/test_api_zeopp.py: 55 passed
• PYTHONPATH=src pytest -q tests/ --ignore=tests/test_mcp_api.py: 410 passed, 1 skipped
• ruff check src tests
• Ruff format check for changed Python files
• python -m build --no-isolation
• git diff --check

Environment notes

• Full test collection requires mcp>=2; the current environment has mcp 1.16.0, so tests/test_mcp_api.py was excluded.
• The repository-wide Ruff format check still identifies pre-existing formatting drift in unchanged tests/test_graspa.py.