refactor(issue-9 phase-5): prune orphaned read_repo_id imports from ~70 command files and test fixtures
- Removed unused read_repo_id import + dead assignment from ~70 command files (age, agent_map, annotate, api_surface, apply_patch, archive, bisect, blame, blast_risk, breakage, cadence, cat, check, checkout_symbol, clones, codemap, compare, content_grep, contour, contract, core_blame, core_cat, coupling, coverage, dead, density, deps, detect_refactor, diff, entangle, find_phrase, find_symbol, forecast, format_patch, gravity, grep, hotspots, impact, instrumentation, invariants, languages, ls_tree, midi_harmony, motif_detect, narrative, note_blame, note_hotspots, note_log, notes, patch_id, piano_roll, plan_merge, predict, query, query_history, read, rename, reset, restore, rev_list, rhythm, scale_detect, semantic_cherry_pick, semantic_test_coverage, shard, shelf, stable, symbol_log, symbols, tempo, tension, velocity, velocity_profile, voice_leading) - Removed dead repo_id param from helper fns: _resolve_start_point (branch.py), _checkout_with_merge (checkout.py), _resolve_refs (bundle.py), _gather_commits (lineage.py), _load (midi_compare.py), _get_manifest (type_cmd.py) - Removed repo_id field from _ReadCommitJson TypedDict and example docstring - Removed stale patch() calls in test_cmd_plan_merge.py and test_cmd_pull_hardening.py that patched symbols no longer present in those modules - Updated test_cmd_branch.py, test_cmd_checkout.py, test_rebase_missing_snapshot_guard.py, test_directories_feature.py to match pruned function signatures
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