[DylanCosto]

Cohort scoring repeatedly subtracted and added contributions for each non-reference sample. Precompute exact differences once per term and skip packed groups of four homozygous-reference samples. Keep the general path for wide coefficients, different dosage-weight exponents, and missing calls, preserving score text and coverage.

On synthetic workloads of two 100,000-term scores and 257 samples, the first five-run comparison reduced scoring time by 22–24% for sparse cohorts and 48% for dense cohorts at 1 and 4 threads. A second comparison confirmed the gain and passed a 15% scoring-regression gate. These are synthetic scoring-only measurements; single-sample gVCF speed was essentially unchanged. See bench/README.md for reproduction and timings.

Add a benchmark runner with an independent integer oracle, exact-output comparisons across binaries and thread counts, wall/CPU time, and peak memory. CI now tests stable Rust on Linux/macOS and Rust 1.88 on Linux, plus a release-mode benchmark smoke test. Release packaging checks the tag against the package version, uses locked tests, smoke-tests native binaries, and includes release notes.

This PR also fixes reference-panel comparison symmetry: terms below 99% panel call rate are excluded from both sides and matched coverage. Score JSON moves to pgsum-score-v3, undefined Z-scores become null, and imputation metadata distinguishes observed scores, sample filling, and reference-panel filling. Public hand-calculated tests and migration notes cover the changes.

Validation:

• Full suite: 87 passed, 1 ignored (external HG002 data), on Rust 1.88 and in release mode on stable Rust.
• cargo fmt --check and cargo clippy --all-targets --locked -- -D warnings: passed.
• Two five-run before/after benchmark comparisons passed the independent oracle and output-equivalence checks.
• Uploaded repository tree exactly matches the locally tested files.

Large real-genome panel comparisons have not been rerun under the exclusion rule. Historical panel results are labeled accordingly. No release tag has been published.