F1's index_refs now builds a code_family_index per run by refreshing pfs.families.FAMILIES from the DuckDB replica when it's on disk. tests/llm/test_index.py didn't mock that (llm.index._code_index), so its index_docs tests ran against the real live replica and permanently mutated the global FAMILIES registry — CCM/APCM picked up real derived codes (G0502, G0503, G2058) that then leaked into unrelated tests (tests/cli/test_pfs_cli.py) whenever both files shared a test run.
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