feat: batch 3 CLI flag audit — merge-base, read-snapshot, read-commit, plan-merge, index, and related tests
- Fully migrate merge_base.py, read_snapshot.py, read_commit.py from partial --format/-f migration to canonical --json/-j (dest=json_out) - Remove _FORMAT_CHOICES and --format/-f arg from all three; replace fmt==text guards with not json_out - _emit_error in merge_base.py: change signature from fmt: str to json_out: bool - Add _short_id = short_id re-export in read_snapshot.py and read_commit.py for unit test compatibility - Fix test_merge_base_supercharge.py: add _mbj helper, convert all JSON-parsing calls from _mb to _mbj, fix TestRegisterFlags with positional args - Fix test_cmd_merge_base.py: add --json to JSON-output tests, fix text-format test, replace --format yaml test with unknown-flag test, fix TestRegisterFlags - Fix test_cmd_read_snapshot.py, test_read_snapshot_supercharge.py: add _rsj helper, replace JSON-parsing calls - Fix test_cmd_read_commit.py, test_read_commit_supercharge.py: add _rcj helper, fix commit_keys envelope exclusion set - Fix test_cmd_plan_merge.py: add json_out= to Namespace creations, fix schema_version→schema - Fix test_cmd_index.py: unpack envelope indexes key, fix schema_version→schema - Fix test_index_supercharge.py: pop timestamp before comparing two invocations - All 385 batch-3 tests pass
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