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1. Commits on Apr 5, 2026

   • Release v4.0.0: Java 25, SMSD 6.11.1, code modernization

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2. Commits on Apr 3, 2026

   • Polish benchmark report: 300 DPI charts, improved reaction images, README links

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   • Release v3.9.0: correctness fixes, memory hardening, golden benchmark report

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   • Log stuck MCS pairs with matcher flags for SMSD debugging

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   • Fix MCS deadlock: poll() timeouts, future cancellation, SMSD 6.10.1

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   • Release v3.9.0: six correctness fixes and publication-grade docs

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   • Fix three correctness and memory issues found in code review

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   • Publish to GitHub Packages on release tags only

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   • Restore MIXTURE to Phase 2 algorithm set

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   • Share mapping executor across reactions; name threads for profiling

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   • Reduce benchmark log verbosity and update output format

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   • Remove unused mixture mapping pass

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   • Reuse matched fragment canonicalization

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   • Lazily compute reaction-center diagnostics

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   • Add benchmark phase diagnostics and scoring gate

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   • Cache connectivity and reduce mapping cache churn

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   • Short-circuit tiny fragment mappings

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   • Skip unchanged mapping pairs and index MCS solutions

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   • Add mapping diagnostics benchmark

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   • Deduplicate structural mapping pairs

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   • Restore stronger README branding

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   • Split fast CI from benchmark workflows

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   • Speed up test workflow and harden mapping canonicalisation

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   • Suppress CDK deprecation and unchecked warnings in compiler config

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   • Bring all docs to v3.8.1: algorithm, changelog, bin README

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   • Release 3.8.1: SMSD 6.9.1, MolGraph canonical SMILES, benchmark refresh

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3. Commits on Apr 2, 2026

   • Fix benchmark table: use chemically-equivalent metric for fair comparison

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   • Make logo link to project repo

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   • Drop Java 17-20 JVM flag incompatible with Java 21

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   • Refresh benchmark numbers post stereo-fix

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   • Fix stereo-blind identity shortcut and remove debug output

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   • Restore README logo banner

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   • Release 3.8.0

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4. Commits on Mar 31, 2026

   • Align all docs, benchmarks, and jar references to v3.7.0

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   • Add formal algorithm description for publication (ALGORITHM.md)

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