Changelog

Unreleased

CLI: bump Helix CLI Session Contract to v2 and stamp contract_id/contract_hash into .helix sessions, *.export.json, and *.png.provenance.json.

Release workflow: build in a clean dist/ so trusted publishing uploads only helix-governance artifacts (no legacy veri_helix-* files).
Packaging: add helix-governance[studio] extra and a helix-studio shim that prints install guidance when GUI deps are missing.
Release assets: placeholder .asc files are non-empty (avoids GitHub Release asset upload failures when GPG is not configured).

Windows release packaging: tolerate PyInstaller _internal/ layout by copying helix_build_meta.json to the app root before zipping.
CLI: add Helix CLI Session Contract v1 (cross-platform E2E gate + deterministic failure-path contract for simulate → report → export).

Windows release packaging: fix EXE(...) wiring in PyInstaller spec (pass TOC iterables, not a single TOC tuple).

Windows release packaging: fix PyInstaller datas shader inclusion (use explicit (src, dest) pairs; no Tree(...) entries).

CI/release: fix .github/workflows/release.yml conditional publish steps so the workflow parses and runs on GitHub Actions.

Windows release packaging: fix PyInstaller datas shader Tree handling (datas += Tree(...), not append).
Release workflow: allow optional API-token publish fallback (secrets PYPI_API_TOKEN / TEST_PYPI_API_TOKEN) to bootstrap new PyPI projects; otherwise uses trusted publishing.

Windows release packaging: fix PyInstaller spec repo-root detection (no __file__ reliance; honors GITHUB_WORKSPACE/HELIX_REPO_ROOT).
Docs: surface helix-governance → helix-governance migration note prominently in README and Getting Started.

Breaking: distribution rename migration path for legacy installs: python -m pip uninstall -y helix-governance && python -m pip install -U helix-governance (module/CLI entrypoints unchanged).
Authority visibility wedge: deterministic provenance header + block injected into *.export.json, *.evidence.json, and HTML reports; Studio surfaces DECISION_GRADE vs EXPLORATORY via readiness gates.
Artifact bundle verifier UX: helix verify <bundle> prepends a human summary (includes short manifest hash even on failure) while preserving stable machine FAIL\t... lines.
Decision-grade export hardening: decision-grade writers fail closed without a signing context; bundle builder plumbs signing through so signed bundles don’t trip SIGNING_KEY_REQUIRED.
Governance onboarding primitive: helix governance self-check (offline, JSON + --strict) reports pinned issuer keys, policy label, license scope, and signing readiness without leaking secrets.

End-to-end design partner funnel: helix partner run now emits three seeded demos + optional support bundle with JSON handshake metadata for easy triage.
Intake automation: tools/partner_intake.py (strict bundle + handshake checks), tools/partner_case.py (case folder + ledger regeneration), and tools/partner_followup.py (templated emails) harden the return path.
Repro bundle v1: repro/helix_repro_bundle_v1 plus CLI helix run --out/helix verify --kind repro keep CPU↔GPU outputs aligned; backend parity tests exercise the bundle in CI.

Studio Lightcone panel with GPU renderer, picking, and selection drilldowns; exports audit-pack zips (manifest + receipts + selection dump) for traceable viz artifacts.
Lightcone perf harness + pinned baseline gate (tools/lightcone_perf.py, tests/test_lightcone_perf_smoke.py) keep shader/geometry changes honest on the pinned GPU runner.
CLI experiment dump accepts Lightcone audit packs (helix experiment dump --audit-pack …) so headless workflows can consume the same fixtures.

Snapshot-driven .helix sessions with headless parity: helix simulate|run writes sessions, helix report/export renders HTML + PNG evidence, and helix engine info/benchmark stamp backend + scoring metadata.
Reproducibility + schema surface: Snapshot Spec v1 published; helixspec compile/diff/run/verify commands added; VeriBiota export/lean-check/preflight wired into the CLI.
Studio spine stabilized: start panel + presets, run history table with compare/export shortcuts, and refreshed Outcome Explorer/Guide Inspector flows (see 0.5.x notes below).

New Start panel + hero status console (running/error/last run) with shortcuts.
Built-in CRISPR & Prime EMX1 demos via experiment presets; user presets save/load/picker.
Outcome Explorer upgrades: chips, prob-mass label, pinned intended row, hover tooltips, selection glow, chart PNG export.
Guides/Compare redesign with run chips, deltas, and baseline/candidate wiring from Run History (B/C shortcuts).
Run History now a styled experiment table with labels, intended/frameshift metrics, relative “When”, rename, export summary.
Layout preset + screenshot helper; onboarding hint banners; keyboard shortcuts dialog expanded.
Tests for hero status, outcome explorer, experiment presets; perf guard for large runs.

Canonical data models: RunModel / OutcomeModel / EngineInfo; SessionModel stores runs; .helix sessions for CLI + Studio interoperability.
Simulation: CRISPR and PRIME via LocalEngine (Studio + helix-cli simulate), with prime knobs (pam_profile, draws, seed) and scenario tagging.
Analysis UX: Guide Inspector (score, rank, filters, scenario column, batch export, compare), Outcome Explorer (chips for cut/no-cut/frameshift|cut, physics, engine, rank, metadata), compare view, PCR CTA, helix highlight.
Reports: GUI and headless HTML export (engine/backend + scoring versions + metadata; CSV/JSON; no-chart tolerant).
Benchmarks: helix-cli bench and Engine Health panel; last bench persisted to ~/.helix/benchmarks.json and shown in Studio.
Persistence: save/load sessions, recent sessions MRU, welcome dialog, demo session bundled (docs/demo/demo_session.helix).
Headless pipeline: helix-cli simulate (CRISPR/Prime, scenarios) → .helix → helix-cli report (optional run-id filter).
Docs: studio tour, headless CLI guide, config schema, validation scaffold.
Tests: CLI simulate/report (CRISPR/Prime), run-id filter, metadata chips, no-chart reporting, engine info, Inspector filters, demo session load, Studio integration.