fix: invalidate chunks when chunkers change

[mikemikimike]

Summary

Invalidates persisted file chunks whenever the configured file chunker output shape changes.

What changed

• Adds stable configuration fingerprints to the built-in file chunkers.
• Versions LocalFileStore chunk persistence with the active chunker fingerprint.
• Versions FAISS and Zvec derived indexes with the same suffix.
• Preserves the legacy v1 filename behavior for standalone stores without an application context.
• Adds regressions for configuration changes, equivalent configuration stability, and legacy snapshot exclusion with graph repair.

Verification

• PYTEST_DISABLE_PLUGIN_AUTOLOAD=1 python -m pytest -p pytest_asyncio.plugin tests/unit/test_chunk_store_fingerprint.py tests/unit/test_file_store_consistency.py tests/unit/test_default_file_chunker.py tests/unit/test_json_file_chunker.py tests/unit/test_jsonl_file_chunker.py -q --deselect tests/unit/test_default_file_chunker.py::test_parse_empty_file
• Result: 169 passed, 12 skipped, 1 deselected
• ruff check passed
• python -m compileall -q reme passed
• git diff --check passed

The one deselected test asserts Windows backslash formatting against a POSIX-normalized path and is unrelated to this change.

Closes #524.