v2.2.0 Audit Closure and Stage Handoff Edition

CHARMM-GUI System Builder v2.2.0

v2.2.0 adds a formal, fail-closed closure between a completed CHARMM-GUI build and any later MD workflow. It preserves the v2.1 guided decision and build-contract workflow while adding immutable Stage 2 evidence and handoff controls.

Major upgrades

• Vendored simulation-stage-contracts v1.0.0 with deterministic file and tree-hash verification.
• Build contract schema 2.2 with non-destructive v2.1 compatibility.
• Evidence dependency and freshness checks that invalidate stale downstream reports.
• Semantic topology and segment reconciliation instead of literal file equality.
• Capability-aware strict grompp plus TPR readback; no -maxwarn bypass.
• Structural-environment parity ledger for resolved lipids, ions, cofactors, and pocket components.
• Pose-preservation evidence with explicit protein/pocket alignment scope.
• Restraint file, macro, equilibration schedule, and release-handoff validation.
• Receipt 2.0 read-only audit, separately authorized atomic lock, independent verification, and hash-chained supersession.
• Public synthetic fixtures replace the historical target-specific case summary.
• Explicit PyYAML and jsonschema runtime dependencies, tested on Python 3.11, 3.12, and 3.13.

Validation

• 130 unit tests passed on Python 3.11, 3.12, and 3.13.
• Agent Skills reference validation passed.
• Package validator and vendored shared-core integrity checks passed.
• README and installation documentation updated for v2.2.0.

Scientific and execution boundary

Every Stage 2 receipt remains production_ready=false, md_execution_allowed=false, and no_mdrun=true. This release does not run MD, approve production, prove a ligand pose, or establish a biological mechanism.

See the README and CHANGELOG for the full migration and evidence model.