refactor(tests): route .muse/ paths through helpers in 8 more files
Fix indices, cmd_verify, cmd_reflog_hardening, cmd_for_each_ref, verify_supercharge, gc_full, core_store, cmd_clean_hardening. Rename self-shadowing locals (ref_path, shelf_dir, indices_dir, muse_dir) and add muse_dir to imports where needed.
sha256:a1dce6fb80fee5a2c34194939f08f070f26871be4f56fef6cbd817a6d19d1888
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sha256:1af3ff9870b55f157592a504a92d1fb5890a97895373b41f5f29574539104536
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