refactor: wire load_json_file and blob_id across all call sites

Replace all json.loads(path.read_text()) patterns with load_json_file(), eliminate manual 'sha256:' + hex string construction in favour of blob_id() and long_id(), and fix pre-existing test failures from the sha256: ID sweep (GcResult.elapsed_seconds → duration_ms, _validate_id accepting sha256: IDs, _sha() helper using blob_id, dag test UUID4 validator updated).

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muse/cli/commands/clone.py::import::datetimemuse/cli/commands/format_patch.py::import::datetimemuse/core/doc_extractor.py::import::datetimemuse/core/indices.py::import::datetimemuse/core/op_log.py::OpLogmuse/core/op_log.py::import::datetimemuse/core/repo.py::import::jsonmuse/core/transport.py::LocalFileTransportmuse/plugins/code/stage.py::import::datetime

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