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

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

RDT v3.8.1 — public release by BioInception PVT LTD

This release marks a significant milestone: core algorithmic and
engineering work developed internally at BioInception is being
made available to the research community, students, and the broader
cheminformatics ecosystem under LGPL v3.

arc: v3.6 → v3.8.1
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Algorithmic advances (proprietary core, now open)
  - Deterministic, training-free reaction atom-atom mapping engine
  - Identity pre-filter: direct atom mapping for unchanged molecules,
    eliminating symmetry-induced spurious bond changes
  - Stereo-correct identity detection using MolGraph canonical SMILES
  - Pre-filter pipeline (identity → atom-count ratio → Tanimoto)
    reducing MCS workload without sacrificing chemistry accuracy
  - Formal algorithm description added (ALGORITHM.md)

Engine & dependency
  - SMSD upgraded 6.7 → 6.9.1 (proprietary BioInception library)
  - Canonical SMILES for identity detection now uses SMSD MolGraph
    (stereo-aware, consistent with internal MCS canonicalisation,
    reduces reliance on CDK SMILES generation)
  - Java 21 full compatibility; CDK 2.12

Quality & validation
  - Golden dataset benchmark (Lin et al. 2022, 1,851 reactions)
  - 99.2% chemically-equivalent atom mapping
  - 76.8% mol-map exact; 99.2% bond-change exact
  - 0 true chemistry misses on first 100 reactions
  - 164 tests, 100% pass

Community
  - Toolkit-agnostic graph model API for CDK / RDKit / OpenBabel
  - Clean one-line Java API (RDT.map())
  - Java 21 build compatibility (CI-validated)
  - Benchmark methodology transparently documented

BioInception PVT LTD — https://www.bioinceptionlabs.com
Author: Dr. Syed Asad Rahman

Release v3.8.0

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

Merge dev: v3.6.1 security hardening, memory fixes, SMSD optimization

Bump RDT version to 3.6.0

Upgrade SMSD to 6.3.0, replace CDK fingerprints with SMSD, update README

- Bump SMSD 5.10.0 to 6.3.0, remove cdk-fingerprint dependency
- GameTheoryEngine: use SMSD.circularFingerprintFCFP with IdentityHashMap cache
- StandardizeReaction: use SMSD.circularFingerprintECFP + fingerprintTanimoto
- Add atom-balance guard to prevent filtering genuine reactants
- README: add RDT logo, update to v3.5.0, SMSD 6.3.0, 163 tests
- All 163 tests pass, no CDK fingerprint imports remain

Revert SMSD to 5.7.1, bump RDT to 3.4.1

SMSD 5.8.x requires Java 21+ (class version 65.0) which breaks CI
on Java 11. Reverting to 5.7.1 for Java 11 compatibility.

Bump RDT version to 3.4.0

New minor version for SMSD 5.8.1 upgrade and dependency updates.
Resolves 409 conflict on GitHub Packages deploy.