fix: systematic test sweep — sha256 prefixes, json_out attrs, envelope keys, legacy migration
Production fixes: - sign.py: rename _SignHeaderJson.timestamp → signing_ts to avoid envelope conflict - query.py: nargs='+' → nargs='*' so bare -j is valid - plugin.py: skip text-merge for binary blobs (b'\x00' detection) - stage.py: add legacy stage.json → msgpack migration in read_stage() - codemap.py, compare.py: add exit_code to JSON fields docstring - bip39.py: mnemonic_to_seed returns bytes not bytearray - ci.py: rename CiRunResult.duration_ms → total_duration_ms - coordination.py: create_reservation/create_intent use compute_*_id (sha256: prefixed); _validate_reservation_id accepts sha256: IDs - symbol_cache.py: _object_id_of uses blob_id() for sha256: prefix
Test fixes: - Replace --format json with --json across show_ref, sign, sign_hardening, remaining, reconcile, reflog_hardening, code_stage - Replace json= with json_out= in Namespace args (coord_data_integrity, coord_performance, coord_pull_null_records, coord_push_null_counts) - Replace bare hex IDs with fake_id()/blob_id() (core_coverage_gaps, core_doc_extractor, core_pack, core_snapshot, core_store, core_symbol_cache, core_validation) - Replace schema_version with schema key in coord_push_null_counts - Fix hashlib import in core_doc_extractor, core_symbol_cache - commit_tree_envelope: add --json flag to invoke call - codemap_supercharge, compare_supercharge: already fixed
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