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Refactoring inventory

This inventory records the final R8 cleanup review. It distinguishes removable debt from compatibility code that only looks obsolete. Public behavior and published binding contracts take precedence over reducing line count.

Removed

  • Five unused direct dependencies: the unwired compressed-pattern dependency, three unused chematic-ewald dependencies, and wasm-bindgen-test in a crate with no Rust wasm-bindgen-test suite.
  • The unreferenced generated compressed SMARTS table. The public compress-patterns feature name remains as a no-op so downstream manifests do not stop resolving.
  • An uncalled private Ewald cutoff implementation hidden behind #[allow(dead_code)].
  • Duplicate Ewald cell-list traversal. Direct and damped cutoff energy now share one private pair iterator while retaining their existing fallback and accumulation rules.

The lockfile no longer carries the dependency closure used only by those declarations.

Retained compatibility paths

  • MCP legacy protocol handling is an advertised wire contract and is exercised by protocol and schema tests.
  • Legacy and accurate CIP modes, named standardization catalogs, and legacy 3D entry points remain public compatibility choices with regression coverage.
  • Generated chemistry tables and ordered rule registries remain data-shaped exceptions. Their order is observable chemistry behavior, so mechanical deduplication or sorting is unsafe.
  • The duplicate deterministic-math traits in chematic-ff and chematic-3d remain crate-private. Sharing them would require a new public cross-crate support API or a new workspace crate; neither is justified by the small, stable implementation.

Audit method

  • Scanned every crate manifest against Rust source, tests, examples, benches, build scripts, target-specific dependencies, and feature references.
  • Searched production Rust for explicit dead-code and unused suppressions, then confirmed references before removal.
  • Ran the refactoring budget ratchet after deleting the stale generated-file exclusion.
  • Verified affected crates with their tests, all-feature/all-target builds, clippy, formatting, and workspace checks described in the main plan.

Future removals should update this inventory only when a compatibility path is actually retired through the normal deprecation policy.