---

page_id: index page_type: index generation_mode: inferred freshness_status: reused updated_at: 2026-07-06T00:27:23.527Z

<details> <summary>Build metadata</summary>

{
  "freshnessKey": "5738e345579d5b313ef1071b74d166eef7028931",
  "plannerReason": "Infra template selected because deterministic evidence suggests deployment or environment configuration is the primary repository surface. The generic runtime page is suppressed because dedicated configuration and troubleshooting pages cover infra setup and operational risk more directly for this repo shape.",
  "changedPaths": [],
  "dependencyPaths": [
    "benchmarks/README.md",
    "deliver_workbench/README.md",
    "deploy/helm/helix-teams/README.md",
    "deploy/k8s/README.md",
    "deploy/README.md",
    "deploy/vastai/README.md",
    "design_partner/README.md",
    "design_partner/sessions/README.md",
    "examples/offscreen_webrtc_demo/signaling/package.json",
    "examples/offscreen_webrtc_demo/signaling/server.js",
    "tools/hubverifier-go/cmd/hubverify/main.go",
    "tools/hubverifier-go/go.mod",
    "engine/src/helix/cuda/fields/composite_editability.cu",
    "engine/src/helix/cuda/fields/dcas9_occupancy.cu",
    "src/helix_api.py",
    "src/helix_cuda_fields.py",
    "src/helix_engine/__init__.py",
    "src/helix_engine/CMakeLists.txt",
    "deliver_workbench/tests/__init__.py",
    "deliver_workbench/tests/test_adapter_e2e.py",
    "deliver_workbench/tests/test_database.py",
    "deliver_workbench/tests/test_matchmaker.py",
    "pyproject.toml",
    "docs/adr/0001-gui-monolith-refactor.md",
    "docs/artifacts.md",
    "docs/assets/viz/alignment-ribbon.json",
    "docs/assets/viz/alignment-ribbon.viz.json",
    "docs/assets/viz/crispr_playground_dag.json",
    "docs/assets/viz/distance-heatmap.json",
    "docs/assets/viz/distance-heatmap.viz.json",
    "docs/assets/viz/minimizers.json",
    "docs/assets/viz/minimizers.viz.json",
    "docs/assets/viz/motif-logo.json",
    "docs/assets/viz/motif-logo.viz.json",
    "docs/assets/viz/pcr_amplicon_dag.json",
    "docs/assets/viz/prime_playground_dag.json",
    "docs/assets/viz/rna-dotplot.json",
    "docs/assets/viz/rna-dotplot.viz.json",
    "docs/assets/viz/seed-chain.json",
    "docs/assets/viz/seed-chain.viz.json",
    "docs/audit_walkthrough.md",
    "docs/battlecards/benchling.md",
    "docs/benchmarks.md",
    "docs/billion_dollar_thesis.md",
    "docs/ci/verify_gate_template.md",
    "docs/ci/verify_reason_codes.md",
    "docs/cli_config_schema.md",
    "docs/cli_headless.md",
    "docs/cli.md",
    "docs/cli/alpha.md",
    "docs/cli/demo.md",
    "docs/cli/live.md",
    "docs/cli/pcr.md",
    "docs/cli/schema.md",
    "docs/cli/session_contract_v1.md",
    "docs/cli/session_contract_v2.md",
    "docs/cli/session_contract_v3.md",
    "docs/cli/viz.md",
    "docs/cli/workflows.md",
    "docs/competitive_landscape.md",
    "docs/concepts/artifacts.md",
    "docs/concepts/multiscale.md",
    "docs/concepts/outcome_digital_twin.md",
    "docs/concepts/perfection.md",
    "docs/concepts/schemas.md",
    "docs/concepts/workflows.md",
    "docs/contracts/enzyme_program_contract_v1.md",
    "docs/contracts/helix_1_0.md",
    "docs/contracts/lightcone_visual_contract_v0_8.md",
    "docs/contributing.md",
    "docs/crispr_ctmc_tau_leap.md",
    "docs/CROSS_HOST_PROTOCOL.md",
    "docs/decision_cockpit_demo.md",
    "docs/decision_support/spec_v0.md",
    "docs/design_partner_email_template.md",
    "docs/design_partner_program.md",
    "docs/dev_gpu_profiling.md",
    "docs/dev/ci_policy.md",
    "docs/dev/evs.md",
    "docs/dev/offtarget_heat.md",
    "docs/dev/packaging_pyinstaller.md",
    "docs/dev/renderer_fields.md",
    "docs/dev/SECURITY_HARDENING.md",
    "docs/dev/SECURITY_SCANNING.md",
    "docs/dev/ui.md",
    "docs/download.md",
    "docs/edit_dag_frames.md",
    "docs/edit_dag_overview.md",
    "docs/edit-dag-viz.md",
    "docs/engine_architecture.md",
    "docs/engine_cuda_plan.md",
    "docs/enterprise_proof/auroc_delta_demo.md",
    "docs/enterprise_proof/azimuth_public.md",
    "docs/enterprise_proof/evaluation_guide.md",
    "docs/enterprise_proof/government-ready-product-surface.md",
    "docs/enterprise_proof/index.md",
    "docs/enterprise_proof/offtarget_public.md",
    "docs/enterprise_proof/roi.md",
    "docs/enterprise_proof/support_policy.md",
    "docs/enterprise_proof/teams_deploy_guide.md",
    "docs/evs_visual_tests.md",
    "docs/evs_visual.md",
    "docs/faq_v0_1.md",
    "docs/features_catalog.md",
    "docs/genome_editing_evidence_runtime_v0_1.md",
    "docs/getting-started.md",
    "docs/governance_contract.md",
    "docs/governed_predictor_adapters.md",
    "docs/helix_experiment_roadmap.md",
    "docs/helix_principles.md",
    "docs/helixspec_mvp.md",
    "docs/helixspec_quickstart.md",
    "docs/hub/end_to_end_v0.md",
    "docs/hub/example_bundle.md",
    "docs/hub/index.md",
    "docs/hub/investor_memo.md",
    "docs/hub/pilot.md",
    "docs/hub/pitch.md",
    "docs/hub/proof_url_v0.md",
    "docs/hub/review_v0.md",
    "docs/hub/rfcs/index.md",
    "docs/hub/rfcs/rfc_0001_bundle_spec_v1.md",
    "docs/hub/rfcs/rfc_0002_canonical_json_v1.md",
    "docs/hub/rfcs/rfc_0003_run_receipt_v1.md",
    "docs/hub/rfcs/rfc_0004_approval_surface_v1.md",
    "docs/hub/rfcs/rfc_0005_approval_receipt_v1.md",
    "docs/hub/rfcs/rfc_0006_audit_export_v1.md",
    "docs/hub/rfcs/rfc_0007_job_v1.md",
    "docs/hub/rfcs/rfc_0008_backend_fingerprint_v1.md",
    "docs/hub/rfcs/rfc_0009_decision_v1.md",
    "docs/hub/trust_model.md",
    "docs/index.md",
    "docs/instructions.md",
    "docs/lightcone_v0_9_milestone.md",
    "docs/model_limitations/crispr_edit_dag_limitations.md",
    "docs/never_do.md",
    "docs/non_goals.md",
    "docs/notebooks/edit_dag_visual_demo.ipynb",
    "docs/ogn_integration.md",
    "docs/omnis_helix_screenshots.md",
    "docs/omnis_helix_strategy.md",
    "docs/omnis_helix_tour.md",
    "docs/paper_deterministic_genome_editing.md",
    "docs/partner_intake.md",
    "docs/partner_ops_playbook.md",
    "docs/playground/index.html",
    "docs/playground/js/realtime_branch_chart.js",
    "docs/playground/js/realtime_compare.js",
    "docs/playground/js/realtime_worker.js",
    "docs/playground/js/realtime.js",
    "docs/playground/realtime.html",
    "docs/policies/compatibility_deprecation.md",
    "docs/policies/conformance.md",
    "docs/policies/export_governance.md",
    "docs/policies/external_attestation.md",
    "docs/policies/governance_registry_policy.md",
    "docs/policies/incident_playbook.md",
    "docs/policies/lean_bridge.md",
    "docs/policies/longevity.md",
    "docs/policies/observability.md",
    "docs/policies/off_target_constraint.md",
    "docs/policies/performance_contracts.md",
    "docs/policies/plugin_governance.md",
    "docs/policies/policy_controls.md",
    "docs/policies/release_provenance.md",
    "docs/policies/schema_hygiene.md",
    "docs/policies/security.md",
    "docs/policies/semantic_drift.md",
    "docs/policies/ux_onboarding.md",
    "docs/positioning.md",
    "docs/prime_physics.md",
    "docs/product_manual.md",
    "docs/proof_bundles.md",
    "docs/proofs/lightcone_demo_proof_v0_8.md",
    "docs/public_release_channel.md",
    "docs/pypi_publishing.md",
    "docs/rail_control_plane.md",
    "docs/reference_validation_bundle.md",
    "docs/reference/api.md",
    "docs/release_checklist.md",
    "docs/RELEASE_VERIFY.md",
    "docs/repo_audit_1b_thesis.json",
    "docs/repo_audit_1b_thesis.md",
    "docs/run_graph.md",
    "docs/run_ingest.md",
    "docs/runbooks/knockout_decision_gate_demo.md",
    "docs/runbooks/lightcone_runbook.md",
    "docs/schema-reference.md",
    "docs/schema.md",
    "docs/scientific_contract_v1.md",
    "docs/scoring_version.md",
    "docs/snapshot_spec_v1.md",
    "docs/snapshot_spec_v1.schema.json",
    "docs/studio/core_features.md",
    "docs/studio/plugins.md",
    "docs/switching_proof_excerpt.txt",
    "docs/switching_proof.md",
    "docs/teams_v0.md",
    "docs/threat_model.md",
    "docs/trust_kit.md",
    "docs/v0_5_milestone.md",
    "docs/validation_crispr_efficiency_panel.md",
    "docs/validation_crispr_offtarget_panel.md",
    "docs/validation_crispr_plasmid.md",
    "docs/validation_prime_panel.md",
    "docs/validation/README.md",
    "docs/veribiota.md",
    "docs/visualization/alignment-ribbon.md",
    "docs/visualization/distance-heatmap.md",
    "docs/visualization/minimizer-density.md",
    "docs/visualization/motif-logo.md",
    "docs/visualization/rna-dotplot.md",
    "docs/viz.md",
    "docs/wetlab_preflight_linter.md",
    "docs/whats-new.md",
    "docs/why_helix.md",
    "examples/delivery/README.md",
    "examples/offscreen_webrtc_demo/README_hw.md",
    "examples/offscreen_webrtc_demo/README.md",
    "examples/plugins/hello_world/README.md",
    "examples/plugins/remote_echo/README.md",
    "examples/plugins/remote_web_panel/README.md",
    "examples/proof/helix_editing_decisions_v1/README.md",
    "examples/README.md",
    "experiments/infrastructure_validation_suite/multi_site_reproducibility/README.md",
    "experiments/infrastructure_validation_suite/procurement_bundles/HELIX_IVS_PROCUREMENT_1.0.0_20260212_173410/README.md",
    "experiments/infrastructure_validation_suite/README.md",
    "experiments/README.md",
    "fixtures/golden_failing_bundle_v1/README.md",
    "fixtures/hostile_bypass_pack_v1/README.md",
    "outreach/README.md",
    "README.md",
    "repro/enzyme_contract_v1/README.md",
    "repro/helix_repro_bundle_v1/README.md",
    "repro/scientific_contract_v1/README.md",
    "schemas/evidence/README.md",
    "schemas/run/README.md",
    "schemas/species/README.md",
    "src/helix/campaigns/README.md",
    "src/helix/compute/README.md",
    "src/helix/datasets/evaluation_packs/helix_eval_v1_azimuth_public/README.md",
    "src/helix/datasets/evaluation_packs/helix_eval_v1_batch_demo/README.md",
    "src/helix/datasets/evaluation_packs/helix_eval_v1_offtarget_public_rloks_sensitive/README.md",
    "src/helix/datasets/evaluation_packs/helix_eval_v1_offtarget_public/README.md",
    "src/helix/datasets/validation_packs/ampseq_indel_profile_v1/README.md",
    "src/helix/datasets/validation_packs/bam_qc_coverage_v1/README.md",
    "src/helix/datasets/validation_packs/cas9_nhej_outcome_prediction_v1/README.md",
    "src/helix/datasets/validation_packs/crisprresso_import_v1/README.md",
    "src/helix/datasets/validation_packs/repro_bundle_v1/README.md",
    "src/helix/datasets/validation_packs/signed_plugin_trust_chain_v1/README.md",
    "src/helix/datasets/validation_packs/vcf_qc_annot_v1/README.md",
    "src/helix/studio/experimental/run_history_mv/README.md",
    "tests/fixtures/lightcone/README.md",
    "tests/systems/fixtures/benchmark_panel/README.md",
    "tests/veribiota/README.md",
    "tools/hubverifier-go/README.md",
    "Visualization_Bench/README.md",
    "requirements-dev.txt",
    "engine/src/helix/cuda/fields/gc_homopolymer.cu",
    "engine/src/helix/cuda/fields/indel_risk.cu",
    "tools/hubverifier-go/internal/c14n/c14n_test.go",
    "tools/hubverifier-go/internal/c14n/c14n.go",
    "src/helix_engine/src/binding.cpp",
    "src/helix_engine/src/ctmc_tau_leap_cuda.cu",
    "src/helix_engine/src/l0_thermo.cu",
    "src/helix_engine/src/physics_cuda.cu"
  ],
  "dependencyEvidenceIds": [
    "component:external:node:express",
    "component:external:node:ws",
    "component:docs",
    "component:pyproject.toml",
    "component:examples/offscreen_webrtc_demo/signaling/package.json",
    "component:src",
    "component:go:tools/hubverifier-go/cmd/hubverify",
    "component:tools/hubverifier-go/go.mod",
    "component:engine/src",
    "ingest:file:src/helix_api.py",
    "ingest:file:src/helix_cuda_fields.py",
    "ingest:file:src/helix_engine/__init__.py",
    "ingest:file:src/helix_engine/CMakeLists.txt",
    "ingest:file:src/helix_engine/include/helix/ctmc_tau_leap_cuda.hpp",
    "ingest:file:src/helix_engine/include/helix/l0_thermo_cuda.hpp",
    "ingest:file:src/helix_engine/include/helix/physics_cuda.hpp",
    "ingest:file:src/helix_engine/include/helix/physics.hpp",
    "ingest:file:src/helix_engine/include/helix/sha256.hpp",
    "ingest:file:src/helix_engine/native.py",
    "ingest:file:deliver_workbench/tests/__init__.py",
    "ingest:file:deliver_workbench/tests/test_adapter_e2e.py",
    "ingest:file:deliver_workbench/tests/test_database.py",
    "ingest:file:deliver_workbench/tests/test_matchmaker.py",
    "ingest:file:experiments/infrastructure_validation_suite/procurement_bundles/HELIX_IVS_PROCUREMENT_1.0.0_20260212_173410/temporal_stability/time_drift_test.sh",
    "ingest:file:experiments/infrastructure_validation_suite/scenarios/synthetic_minimal/minimal_test.json",
    "ingest:file:experiments/infrastructure_validation_suite/temporal_stability/time_drift_test.sh",
    "ingest:file:repro/helix_repro_bundle_v1/inputs/case01.spec.json",
    "ingest:file:scripts/test_golden_workflow.sh",
    "ingest:file:src/helix/datasets/validation_packs/repro_bundle_v1/inputs/case01.spec.json",
    "ingest:file:src/helix/species_test.txt",
    "ingest:file:tests/__init__.py",
    "ingest:file:tests/conftest.py",
    "ingest:file:tests/e2e/test_cli_session_contract_v1.py",
    "ingest:file:tests/e2e/test_cli_session_contract_v2.py",
    "ingest:file:tests/e2e/test_cli_session_contract_v3.py",
    "ingest:file:tests/e2e/test_cli_viz_smoke.py",
    "ingest:file:tests/evs_visual/__init__.py",
    "ingest:file:tests/evs_visual/conftest.py",
    "ingest:file:tests/evs_visual/helpers_composite.py",
    "ingest:file:tests/evs_visual/helpers_gc.py",
    "ingest:file:tests/evs_visual/helpers_indel_risk.py",
    "ingest:file:tests/evs_visual/helpers_offtarget.py",
    "ingest:file:tests/evs_visual/helpers_pam_seed.py",
    "ingest:file:tests/evs_visual/helpers_prime_dp.py",
    "ingest:file:tests/evs_visual/test_composite_lane.py",
    "ingest:file:tests/evs_visual/test_dcas9_lane.py",
    "ingest:file:tests/evs_visual/test_evs_schema_roundtrip.py",
    "ingest:file:tests/evs_visual/test_gc_lane.py",
    "ingest:file:tests/evs_visual/test_indel_risk_lane.py",
    "ingest:file:tests/evs_visual/test_offtarget_density_lane.py",
    "ingest:file:tests/evs_visual/test_pam_seed_lane.py",
    "ingest:file:tests/evs_visual/test_prime_dp_lane.py",
    "ingest:file:tests/evs_visual/test_render.py",
    "ingest:file:tests/evs_visual/v1.0/crispr_basic/crispr_basic.v1.0.evs.json",
    "ingest:file:tests/evs_visual/v1.0/crispr_basic/meta.json",
    "ingest:file:tests/evs_visual/v1.1/evs_composite_lane_v11/evs_composite_lane_v11.v1.1.evs.json",
    "ingest:file:tests/evs_visual/v1.1/evs_composite_lane_v11/meta.json",
    "ingest:file:tests/evs_visual/v1.1/evs_dcas_lane_v11/evs_dcas_lane_v11.v1.1.evs.json",
    "ingest:file:tests/evs_visual/v1.1/evs_dcas_lane_v11/meta.json",
    "ingest:file:tests/evs_visual/v1.1/evs_demo_v11/evs_demo_v11.v1.1.evs.json",
    "ingest:file:tests/evs_visual/v1.1/evs_demo_v11/meta.json",
    "ingest:file:tests/evs_visual/v1.1/evs_gc_lane_v11/evs_gc_lane_v11.v1.1.evs.json",
    "ingest:file:tests/evs_visual/v1.1/evs_gc_lane_v11/meta.json",
    "ingest:file:tests/evs_visual/v1.1/evs_indel_lane_v11/evs_indel_lane_v11.v1.1.evs.json",
    "ingest:file:tests/evs_visual/v1.1/evs_indel_lane_v11/meta.json",
    "ingest:file:tests/evs_visual/v1.1/evs_offtarget_lane_v11/evs_offtarget_lane_v11.v1.1.evs.json",
    "ingest:file:tests/evs_visual/v1.1/evs_offtarget_lane_v11/meta.json",
    "ingest:file:tests/evs_visual/v1.1/evs_prime_lane_v11/evs_prime_lane_v11.v1.1.evs.json",
    "ingest:file:tests/evs_visual/v1.1/evs_prime_lane_v11/meta.json",
    "ingest:file:tests/evs_visual/v1.1/evs_zoom_lane_v11/evs_zoom_lane_v11.v1.1.evs.json",
    "ingest:file:tests/evs_visual/v1.1/evs_zoom_lane_v11/meta.json",
    "ingest:file:tests/evs_visual/v1.1/prime_demo/meta.json",
    "ingest:file:tests/evs_visual/v1.1/prime_demo/prime_demo.v1.1.evs.json",
    "ingest:file:tests/fixtures/assays/assay_plan_case1.json",
    "ingest:file:tests/fixtures/assays/assay_plan_multiplex_case1.json",
    "ingest:file:tests/fixtures/basespace/fastqs.json",
    "ingest:file:tests/fixtures/basespace/run_meta.json",
    "ingest:file:tests/fixtures/batch/batch_genome_case1.json",
    "ingest:file:tests/fixtures/batch/batch_report_case1.json",
    "ingest:file:tests/fixtures/batch/batch_report_pair_case1.json",
    "ingest:file:tests/fixtures/batch/batch_spec_case1.json",
    "ingest:file:tests/fixtures/batch/batch_spec_pair_case1.json",
    "ingest:file:tests/fixtures/calibration_guard/batch_summary.json",
    "ingest:file:tests/fixtures/calibration_guard/pinned_profile.json",
    "ingest:file:tests/fixtures/calibration_guard/records/id1.json",
    "ingest:file:tests/fixtures/calibration/base_position_calibration_eval_case1.json",
    "ingest:file:tests/fixtures/calibration/base_position_calibration_preview_case1.json",
    "ingest:file:tests/fixtures/calibration/base_position_calibration_profile_case1.json",
    "ingest:file:tests/fixtures/calibration/calibration_preview_case1.json",
    "ingest:file:tests/fixtures/calibration/calibration_profile_case1.json",
    "ingest:file:tests/fixtures/contract_info.json",
    "ingest:file:tests/fixtures/ctmc_tau_leap/golden_basic.expected.json",
    "ingest:file:tests/fixtures/ctmc_tau_leap/golden_basic.yaml",
    "ingest:file:tests/fixtures/ctmc_tau_leap/golden_feedback.expected.json",
    "ingest:file:tests/fixtures/ctmc_tau_leap/golden_feedback.yaml",
    "ingest:file:tests/fixtures/ctmc_tau_leap/golden_multilocus.expected.json",
    "ingest:file:tests/fixtures/ctmc_tau_leap/golden_multilocus.yaml",
    "ingest:file:tests/fixtures/edge_config.yaml",
    "ingest:file:tests/fixtures/emx1/decision_v1.json",
    "ingest:file:tests/fixtures/emx1/decision.json",
    "ingest:file:tests/fixtures/emx1/guides.json",
    "ingest:file:tests/fixtures/emx1/target.fa",
    "ingest:file:tests/fixtures/graphs/bubble_reads.fna",
    "ingest:file:tests/fixtures/illumina_run/RTAComplete.txt",
    "ingest:file:tests/fixtures/illumina_run/RunInfo.xml",
    "ingest:file:tests/fixtures/illumina_run/RunParameters.xml",
    "ingest:file:tests/fixtures/illumina_run/SampleSheet.csv",
    "ingest:file:tests/fixtures/ion_torrent/payload.json",
    "ingest:file:tests/fixtures/lightcone/milestone0_prime_with_ghosts.v0.1.json",
    "ingest:file:tests/fixtures/lightcone/milestone1_base_edit_glow.v0.1.json",
    "ingest:file:tests/fixtures/lightcone/milestone1_crispr_messy_cone.v0.1.json",
    "ingest:file:tests/fixtures/lightcone/milestone1_prime_braid_ghosts.v0.1.json",
    "ingest:file:tests/fixtures/lightcone/milestone2_prime_tree_bundled.v0.1.json",
    "ingest:file:tests/fixtures/lightcone/README.md",
    "ingest:file:tests/fixtures/monarchic/tasks_case1.json",
    "ingest:file:tests/fixtures/motifs/simple.fna",
    "ingest:file:tests/fixtures/offtargets/offtarget_case_bulge_input.json",
    "ingest:file:tests/fixtures/offtargets/offtarget_case_bulge_report.json",
    "ingest:file:tests/fixtures/offtargets/offtarget_case_risk_input.json",
    "ingest:file:tests/fixtures/offtargets/offtarget_case_risk_report.json",
    "ingest:file:tests/fixtures/offtargets/offtarget_case_trunc_input.json",
    "ingest:file:tests/fixtures/offtargets/offtarget_case_trunc_report.json",
    "ingest:file:tests/fixtures/offtargets/offtarget_case1_input.json",
    "ingest:file:tests/fixtures/offtargets/offtarget_case1_report.json",
    "ingest:file:tests/fixtures/offtargets/offtarget_multiplex_case1_input.json",
    "ingest:file:tests/fixtures/offtargets/offtarget_multiplex_case1_report.json",
    "ingest:file:tests/fixtures/offtargets/offtarget_rloks_case1_input.json",
    "ingest:file:tests/fixtures/offtargets/offtarget_rloks_case1_report.json",
    "ingest:file:tests/fixtures/offtargets/offtarget_rloks_default_input.json",
    "ingest:file:tests/fixtures/offtargets/offtarget_rloks_default_report.json",
    "ingest:file:tests/fixtures/offtargets/primer_plan_case_risk.json",
    "ingest:file:tests/fixtures/offtargets/primer_plan_multiplex_case1.json",
    "ingest:file:tests/fixtures/offtargets/validation_plan_case_risk.json",
    "ingest:file:tests/fixtures/offtargets/validation_plan_multiplex_case1.json",
    "ingest:file:tests/fixtures/outcomes/base_model_case1_input.json",
    "ingest:file:tests/fixtures/outcomes/base_model_case1_report.json",
    "ingest:file:tests/fixtures/outcomes/base_model_case2_input.json",
    "ingest:file:tests/fixtures/outcomes/base_model_case2_report.json",
    "ingest:file:tests/fixtures/outcomes/clone_plan_case1.json",
    "ingest:file:tests/fixtures/outcomes/cut_model_case1_input.json",
    "ingest:file:tests/fixtures/outcomes/cut_model_case1_report.json",
    "ingest:file:tests/fixtures/outcomes/cut_model_case2_input.json",
    "ingest:file:tests/fixtures/outcomes/cut_model_case2_report.json",
    "ingest:file:tests/fixtures/outcomes/cut_model_case3_input.json",
    "ingest:file:tests/fixtures/outcomes/cut_model_case3_report.json",
    "ingest:file:tests/fixtures/outcomes/multiplex_cut_case_far_input.json",
    "ingest:file:tests/fixtures/outcomes/multiplex_cut_case_far_report.json",
    "ingest:file:tests/fixtures/outcomes/multiplex_cut_case1_input.json",
    "ingest:file:tests/fixtures/outcomes/multiplex_cut_case1_report.json",
    "ingest:file:tests/fixtures/outcomes/noop_outcome_report_v1.json",
    "ingest:file:tests/fixtures/outcomes/prime_model_case1_input.json",
    "ingest:file:tests/fixtures/outcomes/prime_model_case1_report.json",
    "ingest:file:tests/fixtures/outcomes/prime_model_case2_input.json",
    "ingest:file:tests/fixtures/outcomes/prime_model_case2_report.json",
    "ingest:file:tests/fixtures/prime_mux/pinned_profile.json",
    "ingest:file:tests/fixtures/prime_mux/prime_mux_batch_summary.json",
    "ingest:file:tests/fixtures/prime_mux/prime_mux_records.json",
    "ingest:file:tests/fixtures/results/crispresso2/Quantification_window_nucleotide_frequency_table_TEST.txt",
    "ingest:file:tests/fixtures/results/crispresso2/Substitution_frequency_table_around_sgRNA_TEST.txt",
    "ingest:file:tests/fixtures/results/crispresso2/Substitution_frequency_table_TEST.txt",
    "ingest:file:tests/fixtures/results/csv_counts/counts_csv_case1.csv",
    "ingest:file:tests/fixtures/results/csv_counts/counts_csv_case2.csv",
    "ingest:file:tests/fixtures/results/pileup/pileup_case1.txt",
    "ingest:file:tests/fixtures/results/pileup/pileup_case2.txt",
    "ingest:file:tests/fixtures/results/results_record_base_case1.json",
    "ingest:file:tests/fixtures/results/results_record_case1.json",
    "ingest:file:tests/fixtures/results/results_record_counts_csv_case1.json",
    "ingest:file:tests/fixtures/results/results_record_counts_csv_case2.json",
    "ingest:file:tests/fixtures/results/results_record_crispresso2_case1.json",
    "ingest:file:tests/fixtures/results/results_record_crispresso2_full_table.json",
    "ingest:file:tests/fixtures/results/results_record_crispresso2_nf_quant_case1.json",
    "ingest:file:tests/fixtures/results/results_record_pileup_case1.json",
    "ingest:file:tests/fixtures/results/results_record_pileup_case2.json",
    "ingest:file:tests/fixtures/studio/omnis_helix_screenshot_receipt_v1.json",
    "ingest:file:tests/fixtures/suggested_priors/suggested_priors_case1.json",
    "ingest:file:tests/fixtures/teams_audit_export_v1/expected_audit_events.jsonl",
    "ingest:file:tests/fixtures/teams_audit_export_v1/expected_audit_export_v1.json",
    "ingest:file:tests/fixtures/thermo_connect/sample_run/run_completed.json",
    "ingest:file:tests/fixtures/thermo_connect/sample_run/samples.json",
    "ingest:file:tests/fixtures/validation_verdict_vectors/expected.json",
    "ingest:file:tests/fixtures/validation_verdict_vectors/publisher.ed25519",
    "ingest:file:tests/fixtures/validation_verdict_vectors/publisher.pub",
    "ingest:file:tests/fixtures/validation_verdict_vectors/signed_verdict_pretty.json",
    "ingest:file:tests/fixtures/validation_verdict_vectors/signed_verdict.json",
    "ingest:file:tests/fixtures/validation_verdict_vectors/unsigned_payload.json",
    "ingest:file:tests/fixtures/wetlab_preflight/failed_cut_basic.findings.v1.json",
    "ingest:file:tests/fixtures/wetlab_preflight/warnings_cut_basic.findings.v1.json",
    "ingest:file:tests/genome/test_fm_build_wrapper.py",
    "ingest:file:tests/genome/test_fm_registry.py",
    "ingest:file:tests/genome/test_ingest_progress.py",
    "ingest:file:tests/genome/test_parse_percent_sample.py",
    "ingest:file:tests/genome/test_window_iter.py",
    "ingest:file:tests/genome/test_window_store.py",
    "ingest:file:tests/golden/cpu_export/config.json",
    "ingest:file:tests/golden/cpu_minimal/config.json",
    "ingest:file:tests/golden/cpu_minimal/expected_summary.json",
    "ingest:file:tests/golden/edit_dag_proof.json",
    "ingest:file:tests/golden/offtarget/simple_exact_match.json",
    "ingest:file:tests/golden/offtarget/simple_exact.json",
    "ingest:file:tests/release_test_support.py",
    "ingest:file:tests/studio/test_adversarial_semantics.py",
    "ingest:file:tests/studio/test_ansi_parser.py",
    "ingest:file:tests/studio/test_assay_plan.py",
    "ingest:file:tests/studio/test_base_cal_batch_eval.py",
    "ingest:file:tests/studio/test_base_edit_model.py",
    "ingest:file:tests/studio/test_base_overlay.py",
    "ingest:file:tests/studio/test_base_position_calibration.py",
    "ingest:file:tests/studio/test_batch_bundle_auroc.py",
    "ingest:file:tests/studio/test_batch_bundle_determinism.py",
    "ingest:file:tests/studio/test_batch_bundle.py",
    "ingest:file:tests/studio/test_batch_compare_panel.py",
    "ingest:file:tests/studio/test_batch_ingest.py",
    "ingest:file:tests/studio/test_batch_ranking.py",
    "ingest:file:tests/studio/test_batch_runner.py",
    "ingest:file:tests/studio/test_calibration_apply.py",
    "ingest:file:tests/studio/test_calibration_profile.py",
    "ingest:file:tests/studio/test_clone_plan.py",
    "ingest:file:tests/studio/test_console_dock_shell.py",
    "ingest:file:tests/studio/test_crispresso2_adapter.py",
    "ingest:file:tests/studio/test_csv_counts_adapter.py",
    "ingest:file:tests/studio/test_cut_model.py",
    "ingest:file:tests/studio/test_delivery_contract.py",
    "ingest:file:tests/studio/test_dynamic_cut_model.py",
    "ingest:file:tests/studio/test_edit_dag_outcome_review_surface.py",
    "ingest:file:tests/studio/test_edit_dag_panel_actions.py",
    "ingest:file:tests/studio/test_edit_dag_panel_golden.py",
    "ingest:file:tests/studio/test_edit_plan_legacy_bridge.py",
    "ingest:file:tests/studio/test_edit_plan_roundtrip.py",
    "ingest:file:tests/studio/test_empirical_base_position_calibration_e2e.py",
    "ingest:file:tests/studio/test_evs_view_models.py",
    "ingest:file:tests/studio/test_experiment_intent_spec_roundtrip.py",
    "ingest:file:tests/studio/test_experiment_setup_model.py",
    "ingest:file:tests/studio/test_experiment_spec_panel.py",
    "ingest:file:tests/studio/test_experiment_spec_roundtrip.py",
    "ingest:file:tests/studio/test_export_clip.py",
    "ingest:file:tests/studio/test_export_gate_wetlab_preflight.py",
    "ingest:file:tests/studio/test_export_hardening.py",
    "ingest:file:tests/studio/test_fit_to_locus.py",
    "ingest:file:tests/studio/test_helixspec_editor.py",
    "ingest:file:tests/studio/test_hint_banner.py",
    "ingest:file:tests/studio/test_hotspots.py",
    "ingest:file:tests/studio/test_instrument_runs_auto_refresh.py",
    "ingest:file:tests/studio/test_intent_eval.py",
    "ingest:file:tests/studio/test_layout_splitter_persistence.py",
    "ingest:file:tests/studio/test_left_rail_compact_toggle.py",
    "ingest:file:tests/studio/test_lightcone_audit_pack.py",
    "ingest:file:tests/studio/test_lightcone_live.py",
    "ingest:file:tests/studio/test_multiplex_cut_model.py",
    "ingest:file:tests/studio/test_observed_overlay_roundtrip.py",
    "ingest:file:tests/studio/test_offtarget_list_panel.py",
    "ingest:file:tests/studio/test_offtarget_report.py",
    "ingest:file:tests/studio/test_offtarget_risk_scoring.py",
    "ingest:file:tests/studio/test_offtarget_rloks_pack_integrity.py",
    "ingest:file:tests/studio/test_offtarget_rloks_pack_manifest_schema.py",
    "ingest:file:tests/studio/test_offtarget_rloks_pack_manifest.py",
    "ingest:file:tests/studio/test_offtarget_rloks_panel_logic.py",
    "ingest:file:tests/studio/test_offtarget_rloks_provider_hardening.py",
    "ingest:file:tests/studio/test_offtarget_rloks_streaming.py",
    "ingest:file:tests/studio/test_outcome_explorer_header_chevron.py",
    "ingest:file:tests/studio/test_outcome_model_contract.py",
    "ingest:file:tests/studio/test_outcome_spectrum_panel.py",
    "ingest:file:tests/studio/test_outcome_summary_receipt.py",
    "ingest:file:tests/studio/test_pileup_adapter.py",
    "ingest:file:tests/studio/test_pilot_handoff.py",
    "ingest:file:tests/studio/test_pilot_package_ui.py",
    "ingest:file:tests/studio/test_prime_model.py",
    "ingest:file:tests/studio/test_prime_multiplex.py",
    "ingest:file:tests/studio/test_prime_overlay.py",
    "ingest:file:tests/studio/test_primer_plan.py",
    "ingest:file:tests/studio/test_responsive_sizing.py",
    "ingest:file:tests/studio/test_results_panel_batch_eval.py",
    "ingest:file:tests/studio/test_results_panel_batch_ingest.py",
    "ingest:file:tests/studio/test_results_record_io.py",
    "ingest:file:tests/studio/test_run_compare_shell.py",
    "ingest:file:tests/studio/test_run_history_shell.py",
    "ingest:file:tests/studio/test_run_status_panel.py",
    "ingest:file:tests/studio/test_semantic_audit.py",
    "ingest:file:tests/studio/test_semantic_proof.py",
    "ingest:file:tests/studio/test_semantic_schema.py",
    "ingest:file:tests/studio/test_session_drawer_button.py",
    "ingest:file:tests/studio/test_session_inspector_shell.py",
    "ingest:file:tests/studio/test_simulation_diagnostics_panel.py",
    "ingest:file:tests/studio/test_simulation_diagnostics.py",
    "ingest:file:tests/studio/test_sink_ui_helpers.py",
    "ingest:file:tests/studio/test_snap_drift_proof_dialog_smoke.py",
    "ingest:file:tests/studio/test_snap_ui_smoke.py",
    "ingest:file:tests/studio/test_snapshot_to_evs.py",
    "ingest:file:tests/studio/test_spatial_review_panel.py",
    "ingest:file:tests/studio/test_studio_layout_snapshots.py",
    "ingest:file:tests/studio/test_studio_mcp_bridge.py",
    "ingest:file:tests/studio/test_studio_screenshot_receipt.py",
    "ingest:file:tests/studio/test_studio_visualization_snapshot.py",
    "ingest:file:tests/studio/test_suggested_priors_apply.py",
    "ingest:file:tests/studio/test_suggested_priors_compat.py",
    "ingest:file:tests/studio/test_suggested_priors_history_chooser.py",
    "ingest:file:tests/studio/test_suggested_priors.py",
    "ingest:file:tests/studio/test_suggestions_pipeline.py",
    "ingest:file:tests/studio/test_tail_risk_helpers.py",
    "ingest:file:tests/studio/test_tail_risk_panel_model.py",
    "ingest:file:tests/studio/test_text_preview_dialog.py",
    "ingest:file:tests/studio/test_timeline_follow.py",
    "ingest:file:tests/studio/test_validation_plan.py",
    "ingest:file:tests/studio/test_visualization_review_panel.py",
    "ingest:file:tests/systems/__init__.py",
    "ingest:file:tests/systems/fixtures/benchmark_panel/benchmark_panel_manifest.json",
    "ingest:file:tests/systems/fixtures/benchmark_panel/canonical_ambiguous_glial_crispr_low_feasibility.json",
    "ingest:file:tests/systems/fixtures/benchmark_panel/canonical_borderline_motor_neuron_delivery.json",
    "ingest:file:tests/systems/fixtures/benchmark_panel/canonical_negative_csn_neuroimmune_v1.json",
    "ingest:file:tests/systems/fixtures/benchmark_panel/canonical_pass_neuronal_excitability.json",
    "ingest:file:tests/systems/fixtures/benchmark_panel/canonical_pass_oncology_immunotherapy.json",
    "ingest:file:tests/systems/fixtures/benchmark_panel/model_family_registry_entry.json",
    "ingest:file:tests/systems/fixtures/benchmark_panel/README.md",
    "ingest:file:tests/systems/fixtures/benchmark_panel/topology_versioning_contract.json",
    "ingest:file:tests/systems/fixtures/benchmark_panel/TOPOLOGY_VERSIONING_CONTRACT.md",
    "ingest:file:tests/systems/fixtures/benchmark_panel/topology_versioning_rules.json",
    "ingest:file:tests/systems/fixtures/generate_goldens.py",
    "ingest:file:tests/systems/fixtures/golden_bundles/glial_crispr/manifest.json",
    "ingest:file:tests/systems/fixtures/golden_bundles/glial_crispr/network_result.json",
    "ingest:file:tests/systems/fixtures/golden_bundles/glial_crispr/observable_scores.json",
    "ingest:file:tests/systems/fixtures/golden_bundles/glial_crispr/program_score.json",
    "ingest:file:tests/systems/fixtures/golden_bundles/glial_crispr/systems_program.json",
    "ingest:file:tests/systems/fixtures/golden_bundles/glial_crispr/uncertainty_report.json",
    "ingest:file:tests/systems/fixtures/golden_bundles/golden_manifest.json",
    "ingest:file:tests/systems/fixtures/golden_bundles/low_feasibility/manifest.json",
    "ingest:file:tests/systems/fixtures/golden_bundles/low_feasibility/network_result.json",
    "ingest:file:tests/systems/fixtures/golden_bundles/low_feasibility/observable_scores.json",
    "ingest:file:tests/systems/fixtures/golden_bundles/low_feasibility/program_score.json",
    "ingest:file:tests/systems/fixtures/golden_bundles/low_feasibility/systems_program.json",
    "ingest:file:tests/systems/fixtures/golden_bundles/low_feasibility/uncertainty_report.json",
    "ingest:file:tests/systems/fixtures/golden_bundles/neuronal_excitability/manifest.json",
    "ingest:file:tests/systems/fixtures/golden_bundles/neuronal_excitability/network_result.json",
    "ingest:file:tests/systems/fixtures/golden_bundles/neuronal_excitability/observable_scores.json",
    "ingest:file:tests/systems/fixtures/golden_bundles/neuronal_excitability/program_score.json",
    "ingest:file:tests/systems/fixtures/golden_bundles/neuronal_excitability/systems_program.json",
    "ingest:file:tests/systems/fixtures/golden_bundles/neuronal_excitability/uncertainty_report.json",
    "ingest:file:tests/systems/test_acceptance_integration.py",
    "ingest:file:tests/systems/test_acceptance_regression.py",
    "ingest:file:tests/systems/test_bundle.py",
    "ingest:file:tests/systems/test_contracts.py",
    "ingest:file:tests/systems/test_delivery_penalties.py",
    "ingest:file:tests/systems/test_determinism.py",
    "ingest:file:tests/systems/test_disease_models.py",
    "ingest:file:tests/systems/test_drift_sentinel.py",
    "ingest:file:tests/systems/test_propagation.py",
    "ingest:file:tests/systems/test_studio_integration.py",
    "ingest:file:tests/systems/test_threshold_protection.py",
    "ingest:file:tests/systems/test_topology_contract.py",
    "ingest:file:tests/test_alleleops_roundtrip.py",
    "ingest:file:tests/test_analysis_server.py",
    "ingest:file:tests/test_analysis_store.py",
    "ingest:file:tests/test_api_instrument_runs.py",
    "ingest:file:tests/test_artifact_bundle_canonicalization.py",
    "ingest:file:tests/test_artifact_bundle_verify.py",
    "ingest:file:tests/test_artifact_bundle.py",
    "ingest:file:tests/test_basespace_client.py",
    "ingest:file:tests/test_basespace_oauth.py",
    "ingest:file:tests/test_basespace_translator.py",
    "ingest:file:tests/test_benchmark_schema.py",
    "ingest:file:tests/test_bioinformatics.py",
    "ingest:file:tests/test_bool_state_guard.py",
    "ingest:file:tests/test_braid_bundling_invariants.py",
    "ingest:file:tests/test_branch_tree_determinism.py",
    "ingest:file:tests/test_build_evaluation_pack_azimuth.py",
    "ingest:file:tests/test_build_evaluation_pack_offtarget_public.py",
    "ingest:file:tests/test_build_fingerprint_deterministic.py",
    "ingest:file:tests/test_build_meta.py",
    "ingest:file:tests/test_builder_base_v0.py",
    "ingest:file:tests/test_builder_crispr_v0.py",
    "ingest:file:tests/test_builder_prime_v0.py",
    "ingest:file:tests/test_calibration_bundle.py",
    "ingest:file:tests/test_calibration_coverage.py",
    "ingest:file:tests/test_campaigns_cli.py",
    "ingest:file:tests/test_campaigns_determinism.py",
    "ingest:file:tests/test_center_hero_layout.py",
    "ingest:file:tests/test_center_panel_outcome_count.py",
    "ingest:file:tests/test_chain_out_of_order.py",
    "ingest:file:tests/test_claims_dirty_invariant.py",
    "ingest:file:tests/test_cli_completion_footer.py",
    "ingest:file:tests/test_cli_deterministic_smoke.py",
    "ingest:file:tests/test_cli_headless.py",
    "ingest:file:tests/test_cli_helixspec_run.py",
    "ingest:file:tests/test_cli_helixspec.py",
    "ingest:file:tests/test_cli_report_filter.py",
    "ingest:file:tests/test_cli_simulate_prime.py",
    "ingest:file:tests/test_cli_verify_export_contract.py",
    "ingest:file:tests/test_clinical_endpoints.py",
    "ingest:file:tests/test_clinical_protocol.py",
    "ingest:file:tests/test_clinical_replay.py",
    "ingest:file:tests/test_clinical.py",
    "ingest:file:tests/test_codon.py",
    "ingest:file:tests/test_compliance_controls.py",
    "ingest:file:tests/test_composite_editability_cuda.py",
    "ingest:file:tests/test_config_features.py",
    "ingest:file:tests/test_contract_identity_writers.py",
    "ingest:file:tests/test_contract_info.py",
    "ingest:file:tests/test_crash_record.py",
    "ingest:file:tests/test_crispr_backend_selection.py",
    "ingest:file:tests/test_crispr_coordinate_contract.py",
    "ingest:file:tests/test_crispr_cut_position_consistency.py",
    "ingest:file:tests/test_crispr_dag_micro.py",
    "ingest:file:tests/test_crispr_dag_outcomes_sensitive_to_guide.py",
    "ingest:file:tests/test_crispr_decision_contract.py",
    "ingest:file:tests/test_crispr_demo_sim_fixture.py",
    "ingest:file:tests/test_crispr_dynamic_sim.py",
    "ingest:file:tests/test_crispr_edit_class_metadata.py",
    "ingest:file:tests/test_crispr_edit_dag_crispr_micro.py",
    "ingest:file:tests/test_crispr_engine_cuda.py",
    "ingest:file:tests/test_crispr_engine_fixtures.py",
    "ingest:file:tests/test_crispr_fuzz.py",
    "ingest:file:tests/test_crispr_guide_objectives.py",
    "ingest:file:tests/test_crispr_guide_sweep_cli_output.py",
    "ingest:file:tests/test_crispr_guide_sweep.py",
    "ingest:file:tests/test_crispr_guides.py",
    "ingest:file:tests/test_crispr_interaction_proxy.py",
    "ingest:file:tests/test_crispr_native_engine.py",
    "ingest:file:tests/test_crispr_pam_mask.py",
    "ingest:file:tests/test_crispr_pam.py",
    "ingest:file:tests/test_crispr_prove_guide_sweep_cli.py",
    "ingest:file:tests/test_crispr_simulator.py",
    "ingest:file:tests/test_crispr_tau_leap_cli.py",
    "ingest:file:tests/test_crispr_viz_dag_parity.py",
    "ingest:file:tests/test_ctmc_tau_leap_contract.py",
    "ingest:file:tests/test_ctmc_tau_leap_cuda_graphs.py",
    "ingest:file:tests/test_ctmc_tau_leap_divergence_counters.py",
    "ingest:file:tests/test_ctmc_tau_leap_fixtures.py",
    "ingest:file:tests/test_ctmc_tau_leap_gpu_parity_graphs.py",
    "ingest:file:tests/test_ctmc_tau_leap_gpu_parity.py",
    "ingest:file:tests/test_ctmc_tau_leap.py",
    "ingest:file:tests/test_cut_semantics_determinism_property.py",
    "ingest:file:tests/test_cut_semantics.py",
    "ingest:file:tests/test_cut_shift_perturbation.py",
    "ingest:file:tests/test_cyclospectrum.py",
    "ingest:file:tests/test_dcas9_occupancy_cuda.py",
    "ingest:file:tests/test_decision_support_gates_v0.py",
    "ingest:file:tests/test_deltas.py",
    "ingest:file:tests/test_demo_auroc_delta.py",
    "ingest:file:tests/test_demo_session.py",
    "ingest:file:tests/test_determinism_guard.py",
    "ingest:file:tests/test_deterministic_mlp.py",
    "ingest:file:tests/test_deterministic_seq_cnn.py",
    "ingest:file:tests/test_divergence_proof_bundle_reader.py",
    "ingest:file:tests/test_divergence.py",
    "ingest:file:tests/test_download_release_contract.py",
    "ingest:file:tests/test_edge_config.py",
    "ingest:file:tests/test_edge_scratch_cleanup.py",
    "ingest:file:tests/test_edit_dag_display_formatting.py",
    "ingest:file:tests/test_edit_dag_frames.py",
    "ingest:file:tests/test_edit_dag_layout_invariants.py",
    "ingest:file:tests/test_edit_dag.py",
    "ingest:file:tests/test_egfr_grb2_mvp.py",
    "ingest:file:tests/test_egfr_grb2_regression.py",
    "ingest:file:tests/test_enterprise_proof_offtarget_public_doc.py",
    "ingest:file:tests/test_enzyme_contract_v1.py",
    "ingest:file:tests/test_eval_azimuth_pack_auroc.py",
    "ingest:file:tests/test_evaluation_pack_v1.py",
    "ingest:file:tests/test_evaluator_docs_loop_contract.py",
    "ingest:file:tests/test_evaluator_mvp_smoke.py",
    "ingest:file:tests/test_evaluator_release_contract.py",
    "ingest:file:tests/test_event_log.py",
    "ingest:file:tests/test_evidence_view_model.py",
    "ingest:file:tests/test_evs/test_offtarget_heat.py",
    "ingest:file:tests/test_experiment_planner.py",
    "ingest:file:tests/test_experiment_presets.py",
    "ingest:file:tests/test_experiment_setup_dialog.py",
    "ingest:file:tests/test_export_evidence.py",
    "ingest:file:tests/test_export_gate_keys.py",
    "ingest:file:tests/test_export_run.py",
    "ingest:file:tests/test_export_verify.py",
    "ingest:file:tests/test_extension_host_heartbeat.py",
    "ingest:file:tests/test_extension_host.py",
    "ingest:file:tests/test_filter_only_ui_no_ranking.py",
    "ingest:file:tests/test_fm_index.py",
    "ingest:file:tests/test_focus_lens_and_physics.py",
    "ingest:file:tests/test_gate_mode_artifact.py",
    "ingest:file:tests/test_gate_mode_golden_fixtures.py",
    "ingest:file:tests/test_gc_homopolymer_cuda.py",
    "ingest:file:tests/test_genome_editing_evidence_runtime.py",
    "ingest:file:tests/test_geom_builders.py",
    "ingest:file:tests/test_geometry_compiler_determinism.py",
    "ingest:file:tests/test_gl_panel_export_clip.py",
    "ingest:file:tests/test_gl_panel.py",
    "ingest:file:tests/test_golden_failing_bundle_v1.py",
    "ingest:file:tests/test_governance_ledger_v1.py",
    "ingest:file:tests/test_governance_no_side_channels_cli.py",
    "ingest:file:tests/test_governance_repo_balance.py",
    "ingest:file:tests/test_governance_self_check_cli.py",
    "ingest:file:tests/test_governance_watermarking.py",
    "ingest:file:tests/test_gpu_l0_thermo.py",
    "ingest:file:tests/test_graphs_colored.py",
    "ingest:file:tests/test_graphs_dbg.py",
    "ingest:file:tests/test_guide_inspector_model.py",
    "ingest:file:tests/test_helix_api.py",
    "ingest:file:tests/test_helix_cli.py",
    "ingest:file:tests/test_helixspec_canon_hash.py",
    "ingest:file:tests/test_helixspec_diff.py",
    "ingest:file:tests/test_helixspec_lower_engine.py",
    "ingest:file:tests/test_helixspec_parse.py",
    "ingest:file:tests/test_helixspec_typecheck.py",
    "ingest:file:tests/test_hero_status.py",
    "ingest:file:tests/test_hostile_bypass_pack_v1.py",
    "ingest:file:tests/test_hub_cli_hub_root_anywhere.py",
    "ingest:file:tests/test_hub_decision_export_v0.py",
    "ingest:file:tests/test_hub_decision_v1.py",
    "ingest:file:tests/test_hub_example_bundle_v1.py",
    "ingest:file:tests/test_hub_pilot_export_v0.py",
    "ingest:file:tests/test_hub_proof_render_v0.py",
    "ingest:file:tests/test_hub_review_v0.py",
    "ingest:file:tests/test_illumina_translator.py",
    "ingest:file:tests/test_importers_ampseq.py",
    "ingest:file:tests/test_importers_bam.py",
    "ingest:file:tests/test_importers_crispresso.py",
    "ingest:file:tests/test_importers_integration_headless.py",
    "ingest:file:tests/test_importers_registry.py",
    "ingest:file:tests/test_importers_to_run_record.py",
    "ingest:file:tests/test_indel_risk_cuda.py",
    "ingest:file:tests/test_ingest_registry_config.py",
    "ingest:file:tests/test_ingest_status_client.py",
    "ingest:file:tests/test_ingest_status_update_api.py",
    "ingest:file:tests/test_ingest_verification.py",
    "ingest:file:tests/test_instrument_runs_view.py",
    "ingest:file:tests/test_intake_ledger.py",
    "ingest:file:tests/test_integration_studio_project_artifacts.py",
    "ingest:file:tests/test_integration_studio_project_workflow.py",
    "ingest:file:tests/test_integration_studio.py",
    "ingest:file:tests/test_invariants.py",
    "ingest:file:tests/test_ion_receiver_cli.py",
    "ingest:file:tests/test_ion_torrent_receiver.py",
    "ingest:file:tests/test_ion_torrent_translator.py",
    "ingest:file:tests/test_iterated_dynamics.py",
    "ingest:file:tests/test_layout_state.py",
    "ingest:file:tests/test_licensing.py",
    "ingest:file:tests/test_lightcone_3d_view_mode.py",
    "ingest:file:tests/test_lightcone_demo_proof_v0_8.py",
    "ingest:file:tests/test_lightcone_drag_threshold.py",
    "ingest:file:tests/test_lightcone_fixture_schema.py",
    "ingest:file:tests/test_lightcone_gpu_parity.py",
    "ingest:file:tests/test_lightcone_gpu_raster_receipts.py",
    "ingest:file:tests/test_lightcone_panel_smoke.py",
    "ingest:file:tests/test_lightcone_perf_profile.py",
    "ingest:file:tests/test_lightcone_perf_smoke.py",
    "ingest:file:tests/test_lightcone_picking.py",
    "ingest:file:tests/test_lightcone_render_golden.py",
    "ingest:file:tests/test_lightcone_stress_tree_determinism.py",
    "ingest:file:tests/test_live_cli.py",
    "ingest:file:tests/test_main_window_placeholders.py",
    "ingest:file:tests/test_metrics_auroc.py",
    "ingest:file:tests/test_metrics_roi.py",
    "ingest:file:tests/test_mock_run_ingest_server.py",
    "ingest:file:tests/test_modern_engine_time_units.py",
    "ingest:file:tests/test_modern_qt_dpi.py",
    "ingest:file:tests/test_modern_qt_dpr_guardrail.py",
    "ingest:file:tests/test_modern_qt_dpr_resize_click_mapping_guardrail.py",
    "ingest:file:tests/test_modern_qt_pick_alloc_separation_guardrail.py",
    "ingest:file:tests/test_modern_qt_picking_mapping.py",
    "ingest:file:tests/test_modern_qt_render_activation.py",
    "ingest:file:tests/test_modern_qt_resize_alloc_guard.py",
    "ingest:file:tests/test_motif.py",
    "ingest:file:tests/test_nussinov.py",
    "ingest:file:tests/test_offtarget_benchmark.py",
    "ingest:file:tests/test_offtarget_cuda_integration.py",
    "ingest:file:tests/test_offtarget_density_cuda.py",
    "ingest:file:tests/test_offtarget_full_determinism.py",
    "ingest:file:tests/test_offtarget_parity.py",
    "ingest:file:tests/test_offtarget_properties.py",
    "ingest:file:tests/test_ogn_gating.py",
    "ingest:file:tests/test_ogn_manager.py",
    "ingest:file:tests/test_ontargetx_bundle_io.py",
    "ingest:file:tests/test_ontargetx_embedding_v3_kmer2.py",
    "ingest:file:tests/test_ontargetx_embedding_v4_kmer3hash256.py",
    "ingest:file:tests/test_ontargetx_embedding_v4_thermo_positional.py",
    "ingest:file:tests/test_ontargetx_embedding_v5_pos1hot.py",
    "ingest:file:tests/test_ontargetx_embedding_v6_kmer2_thermo.py",
    "ingest:file:tests/test_ontargetx_encoding.py",
    "ingest:file:tests/test_ontargetx_engine_bundle.py",
    "ingest:file:tests/test_ontargetx_ensemble_cv.py",
    "ingest:file:tests/test_ontargetx_governance.py",
    "ingest:file:tests/test_ontargetx_ranking_pairs.py",
    "ingest:file:tests/test_open_snapshot_activates_evs.py",
    "ingest:file:tests/test_optional_deps_errors.py",
    "ingest:file:tests/test_outcome_determinism_permutation.py",
    "ingest:file:tests/test_outcome_explorer_mass.py",
    "ingest:file:tests/test_outcome_explorer.py",
    "ingest:file:tests/test_outcome_flow_intent.py",
    "ingest:file:tests/test_outcome_metadata_chips.py",
    "ingest:file:tests/test_outcome_normalize.py",
    "ingest:file:tests/test_outcome_perturbation_cache.py",
    "ingest:file:tests/test_outcome_posterior.py",
    "ingest:file:tests/test_outcome_ribbon_label_selection.py",
    "ingest:file:tests/test_outcome_space_map.py",
    "ingest:file:tests/test_outcome_stale_drop.py",
    "ingest:file:tests/test_packaging_metadata.py",
    "ingest:file:tests/test_packaging_pyinstaller_doc_contract.py",
    "ingest:file:tests/test_packaging_release_contract.py",
    "ingest:file:tests/test_packaging_trusted_release_contract.py",
    "ingest:file:tests/test_pam_seed_cuda.py",
    "ingest:file:tests/test_partner_followup.py",
    "ingest:file:tests/test_pcr_engine.py",
    "ingest:file:tests/test_phase1_knn.py",
    "ingest:file:tests/test_playground_crispr_micro.py",
    "ingest:file:tests/test_plugin_isolation_rules.py",
    "ingest:file:tests/test_plugin_packages.py",
    "ingest:file:tests/test_plugin_registries.py",
    "ingest:file:tests/test_plugin_registry_cache.py",
    "ingest:file:tests/test_plugins_manager.py",
    "ingest:file:tests/test_plugins_manifest.py",
    "ingest:file:tests/test_policy_packs.py",
    "ingest:file:tests/test_policy_patches.py",
    "ingest:file:tests/test_predictor_receipts.py",
    "ingest:file:tests/test_pricing_enforcement_contract.py",
    "ingest:file:tests/test_prime_dp_cuda.py",
    "ingest:file:tests/test_prime_engine.py",
    "ingest:file:tests/test_prime_multiplex_calibration.py",
    "ingest:file:tests/test_prime_physics_score.py",
    "ingest:file:tests/test_prime_physics.py",
    "ingest:file:tests/test_project_imported_runs.py",
    "ingest:file:tests/test_project_model.py",
    "ingest:file:tests/test_project_snapshot_paths.py",
    "ingest:file:tests/test_project_viz_paths.py",
    "ingest:file:tests/test_proof_kit_builder.py",
    "ingest:file:tests/test_protein.py",
    "ingest:file:tests/test_provenance_headers.py",
    "ingest:file:tests/test_provenance_race.py",
    "ingest:file:tests/test_provenance.py",
    "ingest:file:tests/test_public_release_channel_contract.py",
    "ingest:file:tests/test_public_release_docs_contract.py",
    "ingest:file:tests/test_public_validation_packs_v1.py",
    "ingest:file:tests/test_publish_github_release.py",
    "ingest:file:tests/test_publish_website_release.py",
    "ingest:file:tests/test_pypi_publishing_contract.py",
    "ingest:file:tests/test_qt_headless_import.py",
    "ingest:file:tests/test_rail_health_bar_widget.py",
    "ingest:file:tests/test_rail_state_store.py",
    "ingest:file:tests/test_rail_widget_recompute.py",
    "ingest:file:tests/test_rail_widget_spinner_timer.py",
    "ingest:file:tests/test_realtime_transport.py",
    "ingest:file:tests/test_recompute_chain_policy.py",
    "ingest:file:tests/test_recompute_planner.py",
    "ingest:file:tests/test_reference_validation_bundle_builder.py",
    "ingest:file:tests/test_registry_v1_smoke.py",
    "ingest:file:tests/test_release_asset_provenance_contract.py",
    "ingest:file:tests/test_release_checklist_contract.py",
    "ingest:file:tests/test_release_gates_contract.py",
    "ingest:file:tests/test_release_local.py",
    "ingest:file:tests/test_release_provenance_contract.py",
    "ingest:file:tests/test_release_provenance_statement.py",
    "ingest:file:tests/test_repair_pathways.py",
    "ingest:file:tests/test_repro_adversarial.py",
    "ingest:file:tests/test_repro_backend_parity.py",
    "ingest:file:tests/test_repro_bundle.py",
    "ingest:file:tests/test_repro_filesystem_ordering.py",
    "ingest:file:tests/test_repro_manifest_contract.py",
    "ingest:file:tests/test_repro_subprocess_repeat.py",
    "ingest:file:tests/test_results_adapter_indel_profile.py",
    "ingest:file:tests/test_revenue_plan.py",
    "ingest:file:tests/test_rna_mccaskill.py",
    "ingest:file:tests/test_run_activation_propagates_evs.py",
    "ingest:file:tests/test_run_activation_survives_layout_failure.py",
    "ingest:file:tests/test_run_artifact.py",
    "ingest:file:tests/test_run_bundle.py",
    "ingest:file:tests/test_run_compare_auroc_extract.py",
    "ingest:file:tests/test_run_descriptor_schema.py",
    "ingest:file:tests/test_run_history_mv_repro.py",
    "ingest:file:tests/test_run_history.py",
    "ingest:file:tests/test_run_metrics_json_safe.py",
    "ingest:file:tests/test_run_recorded_updates_analysis_outcome_count.py",
    "ingest:file:tests/test_run_registry_api.py",
    "ingest:file:tests/test_run_registry_status.py",
    "ingest:file:tests/test_run_registry.py",
    "ingest:file:tests/test_s3_blob_store.py",
    "ingest:file:tests/test_save_session_report_writes_file.py",
    "ingest:file:tests/test_scc.py",
    "ingest:file:tests/test_scheduler_islands.py",
    "ingest:file:tests/test_schema_manifest.py",
    "ingest:file:tests/test_scientific_contract.py",
    "ingest:file:tests/test_seed.py",
    "ingest:file:tests/test_selection_utils.py",
    "ingest:file:tests/test_session_model.py",
    "ingest:file:tests/test_session_report_engine_info.py",
    "ingest:file:tests/test_session_report_no_chart.py",
    "ingest:file:tests/test_session_report_watermark.py",
    "ingest:file:tests/test_shipped_ontargetx_v7_manifest.py",
    "ingest:file:tests/test_simbuilder_embedded_layout_smoke.py",
    "ingest:file:tests/test_simbuilder_layout_spacing.py",
    "ingest:file:tests/test_sketch.py",
    "ingest:file:tests/test_smoke_package.py",
    "ingest:file:tests/test_snap_ui_parse_size.py",
    "ingest:file:tests/test_snapshot_bundle.py",
    "ingest:file:tests/test_species_core.py",
    "ingest:file:tests/test_spine_end_to_end.py",
    "ingest:file:tests/test_stage_website_release.py",
    "ingest:file:tests/test_string.py",
    "ingest:file:tests/test_structural_risk.py",
    "ingest:file:tests/test_studio_bootstrap.py",
    "ingest:file:tests/test_studio_core_tabs.py",
    "ingest:file:tests/test_studio_entrypoint.py",
    "ingest:file:tests/test_studio_evaluation_access.py",
    "ingest:file:tests/test_studio_evaluation_gate.py",
    "ingest:file:tests/test_studio_export_parity.py",
    "ingest:file:tests/test_studio_left_tabs_visual_artifact.py",
    "ingest:file:tests/test_studio_plugin_host.py",
    "ingest:file:tests/test_studio_responsiveness.py",
    "ingest:file:tests/test_studio_session_helixspec.py",
    "ingest:file:tests/test_summary_contract_v2.py",
    "ingest:file:tests/test_support_bundle.py",
    "ingest:file:tests/test_sweep.py",
    "ingest:file:tests/test_target_picker_drawer.py",
    "ingest:file:tests/test_target_resolution.py",
    "ingest:file:tests/test_teams_audit_export_v1.py",
    "ingest:file:tests/test_teams_backfill_and_telemetry.py",
    "ingest:file:tests/test_teams_cli_bootstrap.py",
    "ingest:file:tests/test_teams_db_backup.py",
    "ingest:file:tests/test_teams_identity_boundary_docs.py",
    "ingest:file:tests/test_teams_metrics.py",
    "ingest:file:tests/test_teams_oidc_auth.py",
    "ingest:file:tests/test_teams_smoke_contract.py",
    "ingest:file:tests/test_teams_telemetry_seats.py",
    "ingest:file:tests/test_teams_token_policy.py",
    "ingest:file:tests/test_teams_v0_smoke.py",
    "ingest:file:tests/test_theme_stylesheet_smoke.py",
    "ingest:file:tests/test_thermo_connect_translator.py",
    "ingest:file:tests/test_triage.py",
    "ingest:file:tests/test_trust_check_cli.py",
    "ingest:file:tests/test_uploader_streaming.py",
    "ingest:file:tests/test_user_config_profiles.py",
    "ingest:file:tests/test_validate_artifacts.py",
    "ingest:file:tests/test_validation_bundle_verify.py",
    "ingest:file:tests/test_validation_negative_controls.py",
    "ingest:file:tests/test_validation_verdict_vectors.py",
    "ingest:file:tests/test_validation_verdict.py",
    "ingest:file:tests/test_veribiota_checks.py",
    "ingest:file:tests/test_veribiota_cli.py",
    "ingest:file:tests/test_veribiota_export.py",
    "ingest:file:tests/test_verify_fuzz_v1.py",
    "ingest:file:tests/test_verify_pilot_package.py",
    "ingest:file:tests/test_verify_reason_code_contract_v1.py",
    "ingest:file:tests/test_verify_release_provenance.py",
    "ingest:file:tests/test_verify_release_signatures.py",
    "ingest:file:tests/test_viewer_perf_hud_smoke.py",
    "ingest:file:tests/test_visual_diff_report.py",
    "ingest:file:tests/test_web_panel_csp.py",
    "ingest:file:tests/test_web_panel_policy.py",
    "ingest:file:tests/test_web_panels_webengine_smoke.py",
    "ingest:file:tests/test_welcome_dialog_smoke.py",
    "ingest:file:tests/test_wetlab_preflight_linter.py",
    "ingest:file:tests/test_wheel_guard_scroll.py",
    "ingest:file:tests/test_workflow_panel_focus_overlay.py",
    "ingest:file:tests/test_workflow_stats.py",
    "ingest:file:tests/test_workflow2p5d_builder.py",
    "ingest:file:tests/test_zip_artifact_determinism.py",
    "ingest:file:tests/tools/test_batch_eval_base_positions_cli.py",
    "ingest:file:tests/tools/test_batch_eval_leaderboard_cli.py",
    "ingest:file:tests/tools/test_cli_session_contract_runner.py",
    "ingest:file:tests/tools/test_demo_regeneration.py",
    "ingest:file:tests/tools/test_monarchic_repo_balance_cli.py",
    "ingest:file:tests/tools/test_prime_multiplex_leaderboard_cli.py",
    "ingest:file:tests/tools/test_prime_multiplex_leaderboard.py",
    "ingest:file:tests/tools/test_qt_runtime_env.py",
    "ingest:file:tests/tools/test_ship_ontargetx_bundle.py",
    "ingest:file:tests/tools/test_train_ontargetx_bundle_azimuth_cli.py",
    "ingest:file:tests/tools/test_train_ontargetx_bundle_azimuth_hparams.py",
    "ingest:file:tests/tools/test_validate_profiles.py",
    "ingest:file:tests/veribiota/crispr_micro.fna",
    "ingest:file:tests/veribiota/gen_crispr_micro.py",
    "ingest:file:tests/veribiota/gen_pcr_micro.py",
    "ingest:file:tests/veribiota/gen_prime_micro.py",
    "ingest:file:tests/veribiota/pcr_config.json",
    "ingest:file:tests/veribiota/pcr_micro.fna",
    "ingest:file:tests/veribiota/pcr_primers.json",
    "ingest:file:tests/veribiota/prime_editor.json",
    "ingest:file:tests/veribiota/prime_micro.fna",
    "ingest:file:tests/veribiota/prime_peg.json",
    "ingest:file:tests/veribiota/README.md",
    "ingest:file:tests/viz/test_alignment_ribbon_spec.py",
    "ingest:file:tests/viz/test_decision_authority_banner_golden.py",
    "ingest:file:tests/viz/test_distance_heatmap_spec.py",
    "ingest:file:tests/viz/test_minimizers_inputs.py",
    "ingest:file:tests/viz/test_minimizers_spec.py",
    "ingest:file:tests/viz/test_modern_helix_base_count.py",
    "ingest:file:tests/viz/test_modern_qt_helix_reference_golden.py",
    "ingest:file:tests/viz/test_modern_qt_hud_golden.py",
    "ingest:file:tests/viz/test_modern_qt_hud_state_machine.py",
    "ingest:file:tests/viz/test_modern_story_motion_dot_sentinel.py",
    "ingest:file:tests/viz/test_motif_logo_spec.py",
    "ingest:file:tests/viz/test_rail_ribbons_spec.py",
    "ingest:file:tests/viz/test_rna_dotplot_shapes.py",
    "ingest:file:tests/viz/test_rna_dotplot_spec.py",
    "ingest:file:tests/viz/test_seed_chain_spec.py",
    "ingest:file:tools/hubverifier-go/internal/c14n/c14n_test.go",
    "ingest:file:tools/shake_test.py",
    "ingest:file:tools/test_env_guard.py",
    "ingest:file:benchmarks/README.md",
    "ingest:file:deliver_workbench/README.md",
    "ingest:file:deploy/helm/helix-teams/README.md",
    "ingest:file:deploy/k8s/README.md",
    "ingest:file:deploy/README.md",
    "ingest:file:deploy/vastai/README.md",
    "ingest:file:design_partner/README.md",
    "ingest:file:design_partner/sessions/README.md",
    "ingest:file:docs/adr/0001-gui-monolith-refactor.md",
    "ingest:file:docs/artifacts.md",
    "ingest:file:docs/assets/viz/alignment-ribbon.json",
    "ingest:file:docs/assets/viz/alignment-ribbon.viz.json",
    "ingest:file:docs/assets/viz/crispr_playground_dag.json",
    "ingest:file:docs/assets/viz/distance-heatmap.json",
    "ingest:file:docs/assets/viz/distance-heatmap.viz.json",
    "ingest:file:docs/assets/viz/minimizers.json",
    "ingest:file:docs/assets/viz/minimizers.viz.json",
    "ingest:file:docs/assets/viz/motif-logo.json",
    "ingest:file:docs/assets/viz/motif-logo.viz.json",
    "ingest:file:docs/assets/viz/pcr_amplicon_dag.json",
    "ingest:file:docs/assets/viz/prime_playground_dag.json",
    "ingest:file:docs/assets/viz/rna-dotplot.json",
    "ingest:file:docs/assets/viz/rna-dotplot.viz.json",
    "ingest:file:docs/assets/viz/seed-chain.json",
    "ingest:file:docs/assets/viz/seed-chain.viz.json",
    "ingest:file:docs/audit_walkthrough.md",
    "ingest:file:docs/battlecards/benchling.md",
    "ingest:file:docs/benchmarks.md",
    "ingest:file:docs/billion_dollar_thesis.md",
    "ingest:file:docs/ci/verify_gate_template.md",
    "ingest:file:docs/ci/verify_reason_codes.md",
    "ingest:file:docs/cli_config_schema.md",
    "ingest:file:docs/cli_headless.md",
    "ingest:file:docs/cli.md",
    "ingest:file:docs/cli/alpha.md",
    "ingest:file:docs/cli/demo.md",
    "ingest:file:docs/cli/live.md",
    "ingest:file:docs/cli/pcr.md",
    "ingest:file:docs/cli/schema.md",
    "ingest:file:docs/cli/session_contract_v1.md",
    "ingest:file:docs/cli/session_contract_v2.md",
    "ingest:file:docs/cli/session_contract_v3.md",
    "ingest:file:docs/cli/viz.md",
    "ingest:file:docs/cli/workflows.md",
    "ingest:file:docs/competitive_landscape.md",
    "ingest:file:docs/concepts/artifacts.md",
    "ingest:file:docs/concepts/multiscale.md",
    "ingest:file:docs/concepts/outcome_digital_twin.md",
    "ingest:file:docs/concepts/perfection.md",
    "ingest:file:docs/concepts/schemas.md",
    "ingest:file:docs/concepts/workflows.md",
    "ingest:file:docs/contracts/enzyme_program_contract_v1.md",
    "ingest:file:docs/contracts/helix_1_0.md",
    "ingest:file:docs/contracts/lightcone_visual_contract_v0_8.md",
    "ingest:file:docs/contributing.md",
    "ingest:file:docs/crispr_ctmc_tau_leap.md",
    "ingest:file:docs/CROSS_HOST_PROTOCOL.md",
    "ingest:file:docs/decision_cockpit_demo.md",
    "ingest:file:docs/decision_support/spec_v0.md",
    "ingest:file:docs/design_partner_email_template.md",
    "ingest:file:docs/design_partner_program.md",
    "ingest:file:docs/dev_gpu_profiling.md",
    "ingest:file:docs/dev/ci_policy.md",
    "ingest:file:docs/dev/evs.md",
    "ingest:file:docs/dev/offtarget_heat.md",
    "ingest:file:docs/dev/packaging_pyinstaller.md",
    "ingest:file:docs/dev/renderer_fields.md",
    "ingest:file:docs/dev/SECURITY_HARDENING.md",
    "ingest:file:docs/dev/SECURITY_SCANNING.md",
    "ingest:file:docs/dev/ui.md",
    "ingest:file:docs/download.md",
    "ingest:file:docs/edit_dag_frames.md",
    "ingest:file:docs/edit_dag_overview.md",
    "ingest:file:docs/edit-dag-viz.md",
    "ingest:file:docs/engine_architecture.md",
    "ingest:file:docs/engine_cuda_plan.md",
    "ingest:file:docs/enterprise_proof/auroc_delta_demo.md",
    "ingest:file:docs/enterprise_proof/azimuth_public.md",
    "ingest:file:docs/enterprise_proof/evaluation_guide.md",
    "ingest:file:docs/enterprise_proof/government-ready-product-surface.md",
    "ingest:file:docs/enterprise_proof/index.md",
    "ingest:file:docs/enterprise_proof/offtarget_public.md",
    "ingest:file:docs/enterprise_proof/roi.md",
    "ingest:file:docs/enterprise_proof/support_policy.md",
    "ingest:file:docs/enterprise_proof/teams_deploy_guide.md",
    "ingest:file:docs/evs_visual_tests.md",
    "ingest:file:docs/evs_visual.md",
    "ingest:file:docs/faq_v0_1.md",
    "ingest:file:docs/features_catalog.md",
    "ingest:file:docs/genome_editing_evidence_runtime_v0_1.md",
    "ingest:file:docs/getting-started.md",
    "ingest:file:docs/governance_contract.md",
    "ingest:file:docs/governed_predictor_adapters.md",
    "ingest:file:docs/helix_experiment_roadmap.md",
    "ingest:file:docs/helix_principles.md",
    "ingest:file:docs/helixspec_mvp.md",
    "ingest:file:docs/helixspec_quickstart.md",
    "ingest:file:docs/hub/end_to_end_v0.md",
    "ingest:file:docs/hub/example_bundle.md",
    "ingest:file:docs/hub/index.md",
    "ingest:file:docs/hub/investor_memo.md",
    "ingest:file:docs/hub/pilot.md",
    "ingest:file:docs/hub/pitch.md",
    "ingest:file:docs/hub/proof_url_v0.md",
    "ingest:file:docs/hub/review_v0.md",
    "ingest:file:docs/hub/rfcs/index.md",
    "ingest:file:docs/hub/rfcs/rfc_0001_bundle_spec_v1.md",
    "ingest:file:docs/hub/rfcs/rfc_0002_canonical_json_v1.md",
    "ingest:file:docs/hub/rfcs/rfc_0003_run_receipt_v1.md",
    "ingest:file:docs/hub/rfcs/rfc_0004_approval_surface_v1.md",
    "ingest:file:docs/hub/rfcs/rfc_0005_approval_receipt_v1.md",
    "ingest:file:docs/hub/rfcs/rfc_0006_audit_export_v1.md",
    "ingest:file:docs/hub/rfcs/rfc_0007_job_v1.md",
    "ingest:file:docs/hub/rfcs/rfc_0008_backend_fingerprint_v1.md",
    "ingest:file:docs/hub/rfcs/rfc_0009_decision_v1.md",
    "ingest:file:docs/hub/trust_model.md",
    "ingest:file:docs/index.md",
    "ingest:file:docs/instructions.md",
    "ingest:file:docs/lightcone_v0_9_milestone.md",
    "ingest:file:docs/model_limitations/crispr_edit_dag_limitations.md",
    "ingest:file:docs/never_do.md",
    "ingest:file:docs/non_goals.md",
    "ingest:file:docs/notebooks/edit_dag_visual_demo.ipynb",
    "ingest:file:docs/ogn_integration.md",
    "ingest:file:docs/omnis_helix_screenshots.md",
    "ingest:file:docs/omnis_helix_strategy.md",
    "ingest:file:docs/omnis_helix_tour.md",
    "ingest:file:docs/paper_deterministic_genome_editing.md",
    "ingest:file:docs/partner_intake.md",
    "ingest:file:docs/partner_ops_playbook.md",
    "ingest:file:docs/playground/index.html",
    "ingest:file:docs/playground/js/realtime_branch_chart.js",
    "ingest:file:docs/playground/js/realtime_compare.js",
    "ingest:file:docs/playground/js/realtime_worker.js",
    "ingest:file:docs/playground/js/realtime.js",
    "ingest:file:docs/playground/realtime.html",
    "ingest:file:docs/policies/compatibility_deprecation.md",
    "ingest:file:docs/policies/conformance.md",
    "ingest:file:docs/policies/export_governance.md",
    "ingest:file:docs/policies/external_attestation.md",
    "ingest:file:docs/policies/governance_registry_policy.md",
    "ingest:file:docs/policies/incident_playbook.md",
    "ingest:file:docs/policies/lean_bridge.md",
    "ingest:file:docs/policies/longevity.md",
    "ingest:file:docs/policies/observability.md",
    "ingest:file:docs/policies/off_target_constraint.md",
    "ingest:file:docs/policies/performance_contracts.md",
    "ingest:file:docs/policies/plugin_governance.md",
    "ingest:file:docs/policies/policy_controls.md",
    "ingest:file:docs/policies/release_provenance.md",
    "ingest:file:docs/policies/schema_hygiene.md",
    "ingest:file:docs/policies/security.md",
    "ingest:file:docs/policies/semantic_drift.md",
    "ingest:file:docs/policies/ux_onboarding.md",
    "ingest:file:docs/positioning.md",
    "ingest:file:docs/prime_physics.md",
    "ingest:file:docs/product_manual.md",
    "ingest:file:docs/proof_bundles.md",
    "ingest:file:docs/proofs/lightcone_demo_proof_v0_8.md",
    "ingest:file:docs/public_release_channel.md",
    "ingest:file:docs/pypi_publishing.md",
    "ingest:file:docs/rail_control_plane.md",
    "ingest:file:docs/reference_validation_bundle.md",
    "ingest:file:docs/reference/api.md",
    "ingest:file:docs/release_checklist.md",
    "ingest:file:docs/RELEASE_VERIFY.md",
    "ingest:file:docs/repo_audit_1b_thesis.json",
    "ingest:file:docs/repo_audit_1b_thesis.md",
    "ingest:file:docs/run_graph.md",
    "ingest:file:docs/run_ingest.md",
    "ingest:file:docs/runbooks/knockout_decision_gate_demo.md",
    "ingest:file:docs/runbooks/lightcone_runbook.md",
    "ingest:file:docs/schema-reference.md",
    "ingest:file:docs/schema.md",
    "ingest:file:docs/scientific_contract_v1.md",
    "ingest:file:docs/scoring_version.md",
    "ingest:file:docs/snapshot_spec_v1.md",
    "ingest:file:docs/snapshot_spec_v1.schema.json",
    "ingest:file:docs/studio/core_features.md",
    "ingest:file:docs/studio/plugins.md",
    "ingest:file:docs/switching_proof_excerpt.txt",
    "ingest:file:docs/switching_proof.md",
    "ingest:file:docs/teams_v0.md",
    "ingest:file:docs/threat_model.md",
    "ingest:file:docs/trust_kit.md",
    "ingest:file:docs/v0_5_milestone.md",
    "ingest:file:docs/validation_crispr_efficiency_panel.md",
    "ingest:file:docs/validation_crispr_offtarget_panel.md",
    "ingest:file:docs/validation_crispr_plasmid.md",
    "ingest:file:docs/validation_prime_panel.md",
    "ingest:file:docs/validation/README.md",
    "ingest:file:docs/veribiota.md",
    "ingest:file:docs/visualization/alignment-ribbon.md",
    "ingest:file:docs/visualization/distance-heatmap.md",
    "ingest:file:docs/visualization/minimizer-density.md",
    "ingest:file:docs/visualization/motif-logo.md",
    "ingest:file:docs/visualization/rna-dotplot.md",
    "ingest:file:docs/viz.md",
    "ingest:file:docs/wetlab_preflight_linter.md",
    "ingest:file:docs/whats-new.md",
    "ingest:file:docs/why_helix.md",
    "ingest:file:examples/delivery/README.md",
    "ingest:file:examples/offscreen_webrtc_demo/README_hw.md",
    "ingest:file:examples/offscreen_webrtc_demo/README.md",
    "ingest:file:examples/plugins/hello_world/README.md",
    "ingest:file:examples/plugins/remote_echo/README.md",
    "ingest:file:examples/plugins/remote_web_panel/README.md",
    "ingest:file:examples/proof/helix_editing_decisions_v1/README.md",
    "ingest:file:examples/README.md",
    "ingest:file:experiments/infrastructure_validation_suite/multi_site_reproducibility/README.md",
    "ingest:file:experiments/infrastructure_validation_suite/procurement_bundles/HELIX_IVS_PROCUREMENT_1.0.0_20260212_173410/README.md",
    "ingest:file:experiments/infrastructure_validation_suite/README.md",
    "ingest:file:experiments/README.md",
    "ingest:file:fixtures/golden_failing_bundle_v1/README.md",
    "ingest:file:fixtures/hostile_bypass_pack_v1/README.md",
    "ingest:file:outreach/README.md",
    "ingest:file:README.md",
    "ingest:file:repro/enzyme_contract_v1/README.md",
    "ingest:file:repro/helix_repro_bundle_v1/README.md",
    "ingest:file:repro/scientific_contract_v1/README.md",
    "ingest:file:schemas/evidence/README.md",
    "ingest:file:schemas/run/README.md",
    "ingest:file:schemas/species/README.md",
    "ingest:file:src/helix/campaigns/README.md",
    "ingest:file:src/helix/compute/README.md",
    "ingest:file:src/helix/datasets/evaluation_packs/helix_eval_v1_azimuth_public/README.md",
    "ingest:file:src/helix/datasets/evaluation_packs/helix_eval_v1_batch_demo/README.md",
    "ingest:file:src/helix/datasets/evaluation_packs/helix_eval_v1_offtarget_public_rloks_sensitive/README.md",
    "ingest:file:src/helix/datasets/evaluation_packs/helix_eval_v1_offtarget_public/README.md",
    "ingest:file:src/helix/datasets/validation_packs/ampseq_indel_profile_v1/README.md",
    "ingest:file:src/helix/datasets/validation_packs/bam_qc_coverage_v1/README.md",
    "ingest:file:src/helix/datasets/validation_packs/cas9_nhej_outcome_prediction_v1/README.md",
    "ingest:file:src/helix/datasets/validation_packs/crisprresso_import_v1/README.md",
    "ingest:file:src/helix/datasets/validation_packs/repro_bundle_v1/README.md",
    "ingest:file:src/helix/datasets/validation_packs/signed_plugin_trust_chain_v1/README.md",
    "ingest:file:src/helix/datasets/validation_packs/vcf_qc_annot_v1/README.md",
    "ingest:file:src/helix/studio/experimental/run_history_mv/README.md",
    "ingest:file:tools/hubverifier-go/README.md",
    "ingest:file:Visualization_Bench/README.md",
    "component:requirements-dev.txt",
    "ingest:file:engine/src/helix/cuda/fields/composite_editability.cu",
    "ingest:file:engine/src/helix/cuda/fields/dcas9_occupancy.cu",
    "ingest:file:engine/src/helix/cuda/fields/gc_homopolymer.cu",
    "ingest:file:engine/src/helix/cuda/fields/indel_risk.cu",
    "ingest:file:engine/src/helix/cuda/fields/offtarget_density.cu",
    "ingest:file:engine/src/helix/cuda/fields/pam_seed.cu",
    "ingest:file:engine/src/helix/cuda/fields/prime_dp.cu",
    "ingest:file:src/helix_engine/src/binding.cpp",
    "ingest:file:src/helix_engine/src/ctmc_tau_leap_cuda.cu",
    "ingest:file:src/helix_engine/src/l0_thermo.cu",
    "ingest:file:src/helix_engine/src/physics_cuda.cu",
    "ingest:file:src/helix_engine/src/physics.cpp",
    "ingest:file:src/helix_engine/src/sha256.cpp"
  ],
  "evidenceIds": [
    "component:external:node:express",
    "component:external:node:ws",
    "component:docs",
    "component:pyproject.toml",
    "component:examples/offscreen_webrtc_demo/signaling/package.json",
    "component:src",
    "component:go:tools/hubverifier-go/cmd/hubverify",
    "component:tools/hubverifier-go/go.mod",
    "component:engine/src",
    "ingest:file:src/helix_api.py",
    "ingest:file:src/helix_cuda_fields.py",
    "ingest:file:src/helix_engine/__init__.py",
    "ingest:file:src/helix_engine/CMakeLists.txt",
    "ingest:file:src/helix_engine/include/helix/ctmc_tau_leap_cuda.hpp",
    "ingest:file:src/helix_engine/include/helix/l0_thermo_cuda.hpp",
    "ingest:file:src/helix_engine/include/helix/physics_cuda.hpp",
    "ingest:file:src/helix_engine/include/helix/physics.hpp",
    "ingest:file:src/helix_engine/include/helix/sha256.hpp",
    "ingest:file:src/helix_engine/native.py",
    "ingest:file:deliver_workbench/tests/__init__.py",
    "ingest:file:deliver_workbench/tests/test_adapter_e2e.py",
    "ingest:file:deliver_workbench/tests/test_database.py",
    "ingest:file:deliver_workbench/tests/test_matchmaker.py",
    "ingest:file:experiments/infrastructure_validation_suite/procurement_bundles/HELIX_IVS_PROCUREMENT_1.0.0_20260212_173410/temporal_stability/time_drift_test.sh",
    "ingest:file:experiments/infrastructure_validation_suite/scenarios/synthetic_minimal/minimal_test.json",
    "ingest:file:experiments/infrastructure_validation_suite/temporal_stability/time_drift_test.sh",
    "ingest:file:repro/helix_repro_bundle_v1/inputs/case01.spec.json",
    "ingest:file:scripts/test_golden_workflow.sh",
    "ingest:file:src/helix/datasets/validation_packs/repro_bundle_v1/inputs/case01.spec.json",
    "ingest:file:src/helix/species_test.txt",
    "ingest:file:tests/__init__.py",
    "ingest:file:tests/conftest.py",
    "ingest:file:tests/e2e/test_cli_session_contract_v1.py",
    "ingest:file:tests/e2e/test_cli_session_contract_v2.py",
    "ingest:file:tests/e2e/test_cli_session_contract_v3.py",
    "ingest:file:tests/e2e/test_cli_viz_smoke.py",
    "ingest:file:tests/evs_visual/__init__.py",
    "ingest:file:tests/evs_visual/conftest.py",
    "ingest:file:tests/evs_visual/helpers_composite.py",
    "ingest:file:tests/evs_visual/helpers_gc.py",
    "ingest:file:tests/evs_visual/helpers_indel_risk.py",
    "ingest:file:tests/evs_visual/helpers_offtarget.py",
    "ingest:file:tests/evs_visual/helpers_pam_seed.py",
    "ingest:file:tests/evs_visual/helpers_prime_dp.py",
    "ingest:file:tests/evs_visual/test_composite_lane.py",
    "ingest:file:tests/evs_visual/test_dcas9_lane.py",
    "ingest:file:tests/evs_visual/test_evs_schema_roundtrip.py",
    "ingest:file:tests/evs_visual/test_gc_lane.py",
    "ingest:file:tests/evs_visual/test_indel_risk_lane.py",
    "ingest:file:tests/evs_visual/test_offtarget_density_lane.py",
    "ingest:file:tests/evs_visual/test_pam_seed_lane.py",
    "ingest:file:tests/evs_visual/test_prime_dp_lane.py",
    "ingest:file:tests/evs_visual/test_render.py",
    "ingest:file:tests/evs_visual/v1.0/crispr_basic/crispr_basic.v1.0.evs.json",
    "ingest:file:tests/evs_visual/v1.0/crispr_basic/meta.json",
    "ingest:file:tests/evs_visual/v1.1/evs_composite_lane_v11/evs_composite_lane_v11.v1.1.evs.json",
    "ingest:file:tests/evs_visual/v1.1/evs_composite_lane_v11/meta.json",
    "ingest:file:tests/evs_visual/v1.1/evs_dcas_lane_v11/evs_dcas_lane_v11.v1.1.evs.json",
    "ingest:file:tests/evs_visual/v1.1/evs_dcas_lane_v11/meta.json",
    "ingest:file:tests/evs_visual/v1.1/evs_demo_v11/evs_demo_v11.v1.1.evs.json",
    "ingest:file:tests/evs_visual/v1.1/evs_demo_v11/meta.json",
    "ingest:file:tests/evs_visual/v1.1/evs_gc_lane_v11/evs_gc_lane_v11.v1.1.evs.json",
    "ingest:file:tests/evs_visual/v1.1/evs_gc_lane_v11/meta.json",
    "ingest:file:tests/evs_visual/v1.1/evs_indel_lane_v11/evs_indel_lane_v11.v1.1.evs.json",
    "ingest:file:tests/evs_visual/v1.1/evs_indel_lane_v11/meta.json",
    "ingest:file:tests/evs_visual/v1.1/evs_offtarget_lane_v11/evs_offtarget_lane_v11.v1.1.evs.json",
    "ingest:file:tests/evs_visual/v1.1/evs_offtarget_lane_v11/meta.json",
    "ingest:file:tests/evs_visual/v1.1/evs_prime_lane_v11/evs_prime_lane_v11.v1.1.evs.json",
    "ingest:file:tests/evs_visual/v1.1/evs_prime_lane_v11/meta.json",
    "ingest:file:tests/evs_visual/v1.1/evs_zoom_lane_v11/evs_zoom_lane_v11.v1.1.evs.json",
    "ingest:file:tests/evs_visual/v1.1/evs_zoom_lane_v11/meta.json",
    "ingest:file:tests/evs_visual/v1.1/prime_demo/meta.json",
    "ingest:file:tests/evs_visual/v1.1/prime_demo/prime_demo.v1.1.evs.json",
    "ingest:file:tests/fixtures/assays/assay_plan_case1.json",
    "ingest:file:tests/fixtures/assays/assay_plan_multiplex_case1.json",
    "ingest:file:tests/fixtures/basespace/fastqs.json",
    "ingest:file:tests/fixtures/basespace/run_meta.json",
    "ingest:file:tests/fixtures/batch/batch_genome_case1.json",
    "ingest:file:tests/fixtures/batch/batch_report_case1.json",
    "ingest:file:tests/fixtures/batch/batch_report_pair_case1.json",
    "ingest:file:tests/fixtures/batch/batch_spec_case1.json",
    "ingest:file:tests/fixtures/batch/batch_spec_pair_case1.json",
    "ingest:file:tests/fixtures/calibration_guard/batch_summary.json",
    "ingest:file:tests/fixtures/calibration_guard/pinned_profile.json",
    "ingest:file:tests/fixtures/calibration_guard/records/id1.json",
    "ingest:file:tests/fixtures/calibration/base_position_calibration_eval_case1.json",
    "ingest:file:tests/fixtures/calibration/base_position_calibration_preview_case1.json",
    "ingest:file:tests/fixtures/calibration/base_position_calibration_profile_case1.json",
    "ingest:file:tests/fixtures/calibration/calibration_preview_case1.json",
    "ingest:file:tests/fixtures/calibration/calibration_profile_case1.json",
    "ingest:file:tests/fixtures/contract_info.json",
    "ingest:file:tests/fixtures/ctmc_tau_leap/golden_basic.expected.json",
    "ingest:file:tests/fixtures/ctmc_tau_leap/golden_basic.yaml",
    "ingest:file:tests/fixtures/ctmc_tau_leap/golden_feedback.expected.json",
    "ingest:file:tests/fixtures/ctmc_tau_leap/golden_feedback.yaml",
    "ingest:file:tests/fixtures/ctmc_tau_leap/golden_multilocus.expected.json",
    "ingest:file:tests/fixtures/ctmc_tau_leap/golden_multilocus.yaml",
    "ingest:file:tests/fixtures/edge_config.yaml",
    "ingest:file:tests/fixtures/emx1/decision_v1.json",
    "ingest:file:tests/fixtures/emx1/decision.json",
    "ingest:file:tests/fixtures/emx1/guides.json",
    "ingest:file:tests/fixtures/emx1/target.fa",
    "ingest:file:tests/fixtures/graphs/bubble_reads.fna",
    "ingest:file:tests/fixtures/illumina_run/RTAComplete.txt",
    "ingest:file:tests/fixtures/illumina_run/RunInfo.xml",
    "ingest:file:tests/fixtures/illumina_run/RunParameters.xml",
    "ingest:file:tests/fixtures/illumina_run/SampleSheet.csv",
    "ingest:file:tests/fixtures/ion_torrent/payload.json",
    "ingest:file:tests/fixtures/lightcone/milestone0_prime_with_ghosts.v0.1.json",
    "ingest:file:tests/fixtures/lightcone/milestone1_base_edit_glow.v0.1.json",
    "ingest:file:tests/fixtures/lightcone/milestone1_crispr_messy_cone.v0.1.json",
    "ingest:file:tests/fixtures/lightcone/milestone1_prime_braid_ghosts.v0.1.json",
    "ingest:file:tests/fixtures/lightcone/milestone2_prime_tree_bundled.v0.1.json",
    "ingest:file:tests/fixtures/lightcone/README.md",
    "ingest:file:tests/fixtures/monarchic/tasks_case1.json",
    "ingest:file:tests/fixtures/motifs/simple.fna",
    "ingest:file:tests/fixtures/offtargets/offtarget_case_bulge_input.json",
    "ingest:file:tests/fixtures/offtargets/offtarget_case_bulge_report.json",
    "ingest:file:tests/fixtures/offtargets/offtarget_case_risk_input.json",
    "ingest:file:tests/fixtures/offtargets/offtarget_case_risk_report.json",
    "ingest:file:tests/fixtures/offtargets/offtarget_case_trunc_input.json",
    "ingest:file:tests/fixtures/offtargets/offtarget_case_trunc_report.json",
    "ingest:file:tests/fixtures/offtargets/offtarget_case1_input.json",
    "ingest:file:tests/fixtures/offtargets/offtarget_case1_report.json",
    "ingest:file:tests/fixtures/offtargets/offtarget_multiplex_case1_input.json",
    "ingest:file:tests/fixtures/offtargets/offtarget_multiplex_case1_report.json",
    "ingest:file:tests/fixtures/offtargets/offtarget_rloks_case1_input.json",
    "ingest:file:tests/fixtures/offtargets/offtarget_rloks_case1_report.json",
    "ingest:file:tests/fixtures/offtargets/offtarget_rloks_default_input.json",
    "ingest:file:tests/fixtures/offtargets/offtarget_rloks_default_report.json",
    "ingest:file:tests/fixtures/offtargets/primer_plan_case_risk.json",
    "ingest:file:tests/fixtures/offtargets/primer_plan_multiplex_case1.json",
    "ingest:file:tests/fixtures/offtargets/validation_plan_case_risk.json",
    "ingest:file:tests/fixtures/offtargets/validation_plan_multiplex_case1.json",
    "ingest:file:tests/fixtures/outcomes/base_model_case1_input.json",
    "ingest:file:tests/fixtures/outcomes/base_model_case1_report.json",
    "ingest:file:tests/fixtures/outcomes/base_model_case2_input.json",
    "ingest:file:tests/fixtures/outcomes/base_model_case2_report.json",
    "ingest:file:tests/fixtures/outcomes/clone_plan_case1.json",
    "ingest:file:tests/fixtures/outcomes/cut_model_case1_input.json",
    "ingest:file:tests/fixtures/outcomes/cut_model_case1_report.json",
    "ingest:file:tests/fixtures/outcomes/cut_model_case2_input.json",
    "ingest:file:tests/fixtures/outcomes/cut_model_case2_report.json",
    "ingest:file:tests/fixtures/outcomes/cut_model_case3_input.json",
    "ingest:file:tests/fixtures/outcomes/cut_model_case3_report.json",
    "ingest:file:tests/fixtures/outcomes/multiplex_cut_case_far_input.json",
    "ingest:file:tests/fixtures/outcomes/multiplex_cut_case_far_report.json",
    "ingest:file:tests/fixtures/outcomes/multiplex_cut_case1_input.json",
    "ingest:file:tests/fixtures/outcomes/multiplex_cut_case1_report.json",
    "ingest:file:tests/fixtures/outcomes/noop_outcome_report_v1.json",
    "ingest:file:tests/fixtures/outcomes/prime_model_case1_input.json",
    "ingest:file:tests/fixtures/outcomes/prime_model_case1_report.json",
    "ingest:file:tests/fixtures/outcomes/prime_model_case2_input.json",
    "ingest:file:tests/fixtures/outcomes/prime_model_case2_report.json",
    "ingest:file:tests/fixtures/prime_mux/pinned_profile.json",
    "ingest:file:tests/fixtures/prime_mux/prime_mux_batch_summary.json",
    "ingest:file:tests/fixtures/prime_mux/prime_mux_records.json",
    "ingest:file:tests/fixtures/results/crispresso2/Quantification_window_nucleotide_frequency_table_TEST.txt",
    "ingest:file:tests/fixtures/results/crispresso2/Substitution_frequency_table_around_sgRNA_TEST.txt",
    "ingest:file:tests/fixtures/results/crispresso2/Substitution_frequency_table_TEST.txt",
    "ingest:file:tests/fixtures/results/csv_counts/counts_csv_case1.csv",
    "ingest:file:tests/fixtures/results/csv_counts/counts_csv_case2.csv",
    "ingest:file:tests/fixtures/results/pileup/pileup_case1.txt",
    "ingest:file:tests/fixtures/results/pileup/pileup_case2.txt",
    "ingest:file:tests/fixtures/results/results_record_base_case1.json",
    "ingest:file:tests/fixtures/results/results_record_case1.json",
    "ingest:file:tests/fixtures/results/results_record_counts_csv_case1.json",
    "ingest:file:tests/fixtures/results/results_record_counts_csv_case2.json",
    "ingest:file:tests/fixtures/results/results_record_crispresso2_case1.json",
    "ingest:file:tests/fixtures/results/results_record_crispresso2_full_table.json",
    "ingest:file:tests/fixtures/results/results_record_crispresso2_nf_quant_case1.json",
    "ingest:file:tests/fixtures/results/results_record_pileup_case1.json",
    "ingest:file:tests/fixtures/results/results_record_pileup_case2.json",
    "ingest:file:tests/fixtures/studio/omnis_helix_screenshot_receipt_v1.json",
    "ingest:file:tests/fixtures/suggested_priors/suggested_priors_case1.json",
    "ingest:file:tests/fixtures/teams_audit_export_v1/expected_audit_events.jsonl",
    "ingest:file:tests/fixtures/teams_audit_export_v1/expected_audit_export_v1.json",
    "ingest:file:tests/fixtures/thermo_connect/sample_run/run_completed.json",
    "ingest:file:tests/fixtures/thermo_connect/sample_run/samples.json",
    "ingest:file:tests/fixtures/validation_verdict_vectors/expected.json",
    "ingest:file:tests/fixtures/validation_verdict_vectors/publisher.ed25519",
    "ingest:file:tests/fixtures/validation_verdict_vectors/publisher.pub",
    "ingest:file:tests/fixtures/validation_verdict_vectors/signed_verdict_pretty.json",
    "ingest:file:tests/fixtures/validation_verdict_vectors/signed_verdict.json",
    "ingest:file:tests/fixtures/validation_verdict_vectors/unsigned_payload.json",
    "ingest:file:tests/fixtures/wetlab_preflight/failed_cut_basic.findings.v1.json",
    "ingest:file:tests/fixtures/wetlab_preflight/warnings_cut_basic.findings.v1.json",
    "ingest:file:tests/genome/test_fm_build_wrapper.py",
    "ingest:file:tests/genome/test_fm_registry.py",
    "ingest:file:tests/genome/test_ingest_progress.py",
    "ingest:file:tests/genome/test_parse_percent_sample.py",
    "ingest:file:tests/genome/test_window_iter.py",
    "ingest:file:tests/genome/test_window_store.py",
    "ingest:file:tests/golden/cpu_export/config.json",
    "ingest:file:tests/golden/cpu_minimal/config.json",
    "ingest:file:tests/golden/cpu_minimal/expected_summary.json",
    "ingest:file:tests/golden/edit_dag_proof.json",
    "ingest:file:tests/golden/offtarget/simple_exact_match.json",
    "ingest:file:tests/golden/offtarget/simple_exact.json",
    "ingest:file:tests/release_test_support.py",
    "ingest:file:tests/studio/test_adversarial_semantics.py",
    "ingest:file:tests/studio/test_ansi_parser.py",
    "ingest:file:tests/studio/test_assay_plan.py",
    "ingest:file:tests/studio/test_base_cal_batch_eval.py",
    "ingest:file:tests/studio/test_base_edit_model.py",
    "ingest:file:tests/studio/test_base_overlay.py",
    "ingest:file:tests/studio/test_base_position_calibration.py",
    "ingest:file:tests/studio/test_batch_bundle_auroc.py",
    "ingest:file:tests/studio/test_batch_bundle_determinism.py",
    "ingest:file:tests/studio/test_batch_bundle.py",
    "ingest:file:tests/studio/test_batch_compare_panel.py",
    "ingest:file:tests/studio/test_batch_ingest.py",
    "ingest:file:tests/studio/test_batch_ranking.py",
    "ingest:file:tests/studio/test_batch_runner.py",
    "ingest:file:tests/studio/test_calibration_apply.py",
    "ingest:file:tests/studio/test_calibration_profile.py",
    "ingest:file:tests/studio/test_clone_plan.py",
    "ingest:file:tests/studio/test_console_dock_shell.py",
    "ingest:file:tests/studio/test_crispresso2_adapter.py",
    "ingest:file:tests/studio/test_csv_counts_adapter.py",
    "ingest:file:tests/studio/test_cut_model.py",
    "ingest:file:tests/studio/test_delivery_contract.py",
    "ingest:file:tests/studio/test_dynamic_cut_model.py",
    "ingest:file:tests/studio/test_edit_dag_outcome_review_surface.py",
    "ingest:file:tests/studio/test_edit_dag_panel_actions.py",
    "ingest:file:tests/studio/test_edit_dag_panel_golden.py",
    "ingest:file:tests/studio/test_edit_plan_legacy_bridge.py",
    "ingest:file:tests/studio/test_edit_plan_roundtrip.py",
    "ingest:file:tests/studio/test_empirical_base_position_calibration_e2e.py",
    "ingest:file:tests/studio/test_evs_view_models.py",
    "ingest:file:tests/studio/test_experiment_intent_spec_roundtrip.py",
    "ingest:file:tests/studio/test_experiment_setup_model.py",
    "ingest:file:tests/studio/test_experiment_spec_panel.py",
    "ingest:file:tests/studio/test_experiment_spec_roundtrip.py",
    "ingest:file:tests/studio/test_export_clip.py",
    "ingest:file:tests/studio/test_export_gate_wetlab_preflight.py",
    "ingest:file:tests/studio/test_export_hardening.py",
    "ingest:file:tests/studio/test_fit_to_locus.py",
    "ingest:file:tests/studio/test_helixspec_editor.py",
    "ingest:file:tests/studio/test_hint_banner.py",
    "ingest:file:tests/studio/test_hotspots.py",
    "ingest:file:tests/studio/test_instrument_runs_auto_refresh.py",
    "ingest:file:tests/studio/test_intent_eval.py",
    "ingest:file:tests/studio/test_layout_splitter_persistence.py",
    "ingest:file:tests/studio/test_left_rail_compact_toggle.py",
    "ingest:file:tests/studio/test_lightcone_audit_pack.py",
    "ingest:file:tests/studio/test_lightcone_live.py",
    "ingest:file:tests/studio/test_multiplex_cut_model.py",
    "ingest:file:tests/studio/test_observed_overlay_roundtrip.py",
    "ingest:file:tests/studio/test_offtarget_list_panel.py",
    "ingest:file:tests/studio/test_offtarget_report.py",
    "ingest:file:tests/studio/test_offtarget_risk_scoring.py",
    "ingest:file:tests/studio/test_offtarget_rloks_pack_integrity.py",
    "ingest:file:tests/studio/test_offtarget_rloks_pack_manifest_schema.py",
    "ingest:file:tests/studio/test_offtarget_rloks_pack_manifest.py",
    "ingest:file:tests/studio/test_offtarget_rloks_panel_logic.py",
    "ingest:file:tests/studio/test_offtarget_rloks_provider_hardening.py",
    "ingest:file:tests/studio/test_offtarget_rloks_streaming.py",
    "ingest:file:tests/studio/test_outcome_explorer_header_chevron.py",
    "ingest:file:tests/studio/test_outcome_model_contract.py",
    "ingest:file:tests/studio/test_outcome_spectrum_panel.py",
    "ingest:file:tests/studio/test_outcome_summary_receipt.py",
    "ingest:file:tests/studio/test_pileup_adapter.py",
    "ingest:file:tests/studio/test_pilot_handoff.py",
    "ingest:file:tests/studio/test_pilot_package_ui.py",
    "ingest:file:tests/studio/test_prime_model.py",
    "ingest:file:tests/studio/test_prime_multiplex.py",
    "ingest:file:tests/studio/test_prime_overlay.py",
    "ingest:file:tests/studio/test_primer_plan.py",
    "ingest:file:tests/studio/test_responsive_sizing.py",
    "ingest:file:tests/studio/test_results_panel_batch_eval.py",
    "ingest:file:tests/studio/test_results_panel_batch_ingest.py",
    "ingest:file:tests/studio/test_results_record_io.py",
    "ingest:file:tests/studio/test_run_compare_shell.py",
    "ingest:file:tests/studio/test_run_history_shell.py",
    "ingest:file:tests/studio/test_run_status_panel.py",
    "ingest:file:tests/studio/test_semantic_audit.py",
    "ingest:file:tests/studio/test_semantic_proof.py",
    "ingest:file:tests/studio/test_semantic_schema.py",
    "ingest:file:tests/studio/test_session_drawer_button.py",
    "ingest:file:tests/studio/test_session_inspector_shell.py",
    "ingest:file:tests/studio/test_simulation_diagnostics_panel.py",
    "ingest:file:tests/studio/test_simulation_diagnostics.py",
    "ingest:file:tests/studio/test_sink_ui_helpers.py",
    "ingest:file:tests/studio/test_snap_drift_proof_dialog_smoke.py",
    "ingest:file:tests/studio/test_snap_ui_smoke.py",
    "ingest:file:tests/studio/test_snapshot_to_evs.py",
    "ingest:file:tests/studio/test_spatial_review_panel.py",
    "ingest:file:tests/studio/test_studio_layout_snapshots.py",
    "ingest:file:tests/studio/test_studio_mcp_bridge.py",
    "ingest:file:tests/studio/test_studio_screenshot_receipt.py",
    "ingest:file:tests/studio/test_studio_visualization_snapshot.py",
    "ingest:file:tests/studio/test_suggested_priors_apply.py",
    "ingest:file:tests/studio/test_suggested_priors_compat.py",
    "ingest:file:tests/studio/test_suggested_priors_history_chooser.py",
    "ingest:file:tests/studio/test_suggested_priors.py",
    "ingest:file:tests/studio/test_suggestions_pipeline.py",
    "ingest:file:tests/studio/test_tail_risk_helpers.py",
    "ingest:file:tests/studio/test_tail_risk_panel_model.py",
    "ingest:file:tests/studio/test_text_preview_dialog.py",
    "ingest:file:tests/studio/test_timeline_follow.py",
    "ingest:file:tests/studio/test_validation_plan.py",
    "ingest:file:tests/studio/test_visualization_review_panel.py",
    "ingest:file:tests/systems/__init__.py",
    "ingest:file:tests/systems/fixtures/benchmark_panel/benchmark_panel_manifest.json",
    "ingest:file:tests/systems/fixtures/benchmark_panel/canonical_ambiguous_glial_crispr_low_feasibility.json",
    "ingest:file:tests/systems/fixtures/benchmark_panel/canonical_borderline_motor_neuron_delivery.json",
    "ingest:file:tests/systems/fixtures/benchmark_panel/canonical_negative_csn_neuroimmune_v1.json",
    "ingest:file:tests/systems/fixtures/benchmark_panel/canonical_pass_neuronal_excitability.json",
    "ingest:file:tests/systems/fixtures/benchmark_panel/canonical_pass_oncology_immunotherapy.json",
    "ingest:file:tests/systems/fixtures/benchmark_panel/model_family_registry_entry.json",
    "ingest:file:tests/systems/fixtures/benchmark_panel/README.md",
    "ingest:file:tests/systems/fixtures/benchmark_panel/topology_versioning_contract.json",
    "ingest:file:tests/systems/fixtures/benchmark_panel/TOPOLOGY_VERSIONING_CONTRACT.md",
    "ingest:file:tests/systems/fixtures/benchmark_panel/topology_versioning_rules.json",
    "ingest:file:tests/systems/fixtures/generate_goldens.py",
    "ingest:file:tests/systems/fixtures/golden_bundles/glial_crispr/manifest.json",
    "ingest:file:tests/systems/fixtures/golden_bundles/glial_crispr/network_result.json",
    "ingest:file:tests/systems/fixtures/golden_bundles/glial_crispr/observable_scores.json",
    "ingest:file:tests/systems/fixtures/golden_bundles/glial_crispr/program_score.json",
    "ingest:file:tests/systems/fixtures/golden_bundles/glial_crispr/systems_program.json",
    "ingest:file:tests/systems/fixtures/golden_bundles/glial_crispr/uncertainty_report.json",
    "ingest:file:tests/systems/fixtures/golden_bundles/golden_manifest.json",
    "ingest:file:tests/systems/fixtures/golden_bundles/low_feasibility/manifest.json",
    "ingest:file:tests/systems/fixtures/golden_bundles/low_feasibility/network_result.json",
    "ingest:file:tests/systems/fixtures/golden_bundles/low_feasibility/observable_scores.json",
    "ingest:file:tests/systems/fixtures/golden_bundles/low_feasibility/program_score.json",
    "ingest:file:tests/systems/fixtures/golden_bundles/low_feasibility/systems_program.json",
    "ingest:file:tests/systems/fixtures/golden_bundles/low_feasibility/uncertainty_report.json",
    "ingest:file:tests/systems/fixtures/golden_bundles/neuronal_excitability/manifest.json",
    "ingest:file:tests/systems/fixtures/golden_bundles/neuronal_excitability/network_result.json",
    "ingest:file:tests/systems/fixtures/golden_bundles/neuronal_excitability/observable_scores.json",
    "ingest:file:tests/systems/fixtures/golden_bundles/neuronal_excitability/program_score.json",
    "ingest:file:tests/systems/fixtures/golden_bundles/neuronal_excitability/systems_program.json",
    "ingest:file:tests/systems/fixtures/golden_bundles/neuronal_excitability/uncertainty_report.json",
    "ingest:file:tests/systems/test_acceptance_integration.py",
    "ingest:file:tests/systems/test_acceptance_regression.py",
    "ingest:file:tests/systems/test_bundle.py",
    "ingest:file:tests/systems/test_contracts.py",
    "ingest:file:tests/systems/test_delivery_penalties.py",
    "ingest:file:tests/systems/test_determinism.py",
    "ingest:file:tests/systems/test_disease_models.py",
    "ingest:file:tests/systems/test_drift_sentinel.py",
    "ingest:file:tests/systems/test_propagation.py",
    "ingest:file:tests/systems/test_studio_integration.py",
    "ingest:file:tests/systems/test_threshold_protection.py",
    "ingest:file:tests/systems/test_topology_contract.py",
    "ingest:file:tests/test_alleleops_roundtrip.py",
    "ingest:file:tests/test_analysis_server.py",
    "ingest:file:tests/test_analysis_store.py",
    "ingest:file:tests/test_api_instrument_runs.py",
    "ingest:file:tests/test_artifact_bundle_canonicalization.py",
    "ingest:file:tests/test_artifact_bundle_verify.py",
    "ingest:file:tests/test_artifact_bundle.py",
    "ingest:file:tests/test_basespace_client.py",
    "ingest:file:tests/test_basespace_oauth.py",
    "ingest:file:tests/test_basespace_translator.py",
    "ingest:file:tests/test_benchmark_schema.py",
    "ingest:file:tests/test_bioinformatics.py",
    "ingest:file:tests/test_bool_state_guard.py",
    "ingest:file:tests/test_braid_bundling_invariants.py",
    "ingest:file:tests/test_branch_tree_determinism.py",
    "ingest:file:tests/test_build_evaluation_pack_azimuth.py",
    "ingest:file:tests/test_build_evaluation_pack_offtarget_public.py",
    "ingest:file:tests/test_build_fingerprint_deterministic.py",
    "ingest:file:tests/test_build_meta.py",
    "ingest:file:tests/test_builder_base_v0.py",
    "ingest:file:tests/test_builder_crispr_v0.py",
    "ingest:file:tests/test_builder_prime_v0.py",
    "ingest:file:tests/test_calibration_bundle.py",
    "ingest:file:tests/test_calibration_coverage.py",
    "ingest:file:tests/test_campaigns_cli.py",
    "ingest:file:tests/test_campaigns_determinism.py",
    "ingest:file:tests/test_center_hero_layout.py",
    "ingest:file:tests/test_center_panel_outcome_count.py",
    "ingest:file:tests/test_chain_out_of_order.py",
    "ingest:file:tests/test_claims_dirty_invariant.py",
    "ingest:file:tests/test_cli_completion_footer.py",
    "ingest:file:tests/test_cli_deterministic_smoke.py",
    "ingest:file:tests/test_cli_headless.py",
    "ingest:file:tests/test_cli_helixspec_run.py",
    "ingest:file:tests/test_cli_helixspec.py",
    "ingest:file:tests/test_cli_report_filter.py",
    "ingest:file:tests/test_cli_simulate_prime.py",
    "ingest:file:tests/test_cli_verify_export_contract.py",
    "ingest:file:tests/test_clinical_endpoints.py",
    "ingest:file:tests/test_clinical_protocol.py",
    "ingest:file:tests/test_clinical_replay.py",
    "ingest:file:tests/test_clinical.py",
    "ingest:file:tests/test_codon.py",
    "ingest:file:tests/test_compliance_controls.py",
    "ingest:file:tests/test_composite_editability_cuda.py",
    "ingest:file:tests/test_config_features.py",
    "ingest:file:tests/test_contract_identity_writers.py",
    "ingest:file:tests/test_contract_info.py",
    "ingest:file:tests/test_crash_record.py",
    "ingest:file:tests/test_crispr_backend_selection.py",
    "ingest:file:tests/test_crispr_coordinate_contract.py",
    "ingest:file:tests/test_crispr_cut_position_consistency.py",
    "ingest:file:tests/test_crispr_dag_micro.py",
    "ingest:file:tests/test_crispr_dag_outcomes_sensitive_to_guide.py",
    "ingest:file:tests/test_crispr_decision_contract.py",
    "ingest:file:tests/test_crispr_demo_sim_fixture.py",
    "ingest:file:tests/test_crispr_dynamic_sim.py",
    "ingest:file:tests/test_crispr_edit_class_metadata.py",
    "ingest:file:tests/test_crispr_edit_dag_crispr_micro.py",
    "ingest:file:tests/test_crispr_engine_cuda.py",
    "ingest:file:tests/test_crispr_engine_fixtures.py",
    "ingest:file:tests/test_crispr_fuzz.py",
    "ingest:file:tests/test_crispr_guide_objectives.py",
    "ingest:file:tests/test_crispr_guide_sweep_cli_output.py",
    "ingest:file:tests/test_crispr_guide_sweep.py",
    "ingest:file:tests/test_crispr_guides.py",
    "ingest:file:tests/test_crispr_interaction_proxy.py",
    "ingest:file:tests/test_crispr_native_engine.py",
    "ingest:file:tests/test_crispr_pam_mask.py",
    "ingest:file:tests/test_crispr_pam.py",
    "ingest:file:tests/test_crispr_prove_guide_sweep_cli.py",
    "ingest:file:tests/test_crispr_simulator.py",
    "ingest:file:tests/test_crispr_tau_leap_cli.py",
    "ingest:file:tests/test_crispr_viz_dag_parity.py",
    "ingest:file:tests/test_ctmc_tau_leap_contract.py",
    "ingest:file:tests/test_ctmc_tau_leap_cuda_graphs.py",
    "ingest:file:tests/test_ctmc_tau_leap_divergence_counters.py",
    "ingest:file:tests/test_ctmc_tau_leap_fixtures.py",
    "ingest:file:tests/test_ctmc_tau_leap_gpu_parity_graphs.py",
    "ingest:file:tests/test_ctmc_tau_leap_gpu_parity.py",
    "ingest:file:tests/test_ctmc_tau_leap.py",
    "ingest:file:tests/test_cut_semantics_determinism_property.py",
    "ingest:file:tests/test_cut_semantics.py",
    "ingest:file:tests/test_cut_shift_perturbation.py",
    "ingest:file:tests/test_cyclospectrum.py",
    "ingest:file:tests/test_dcas9_occupancy_cuda.py",
    "ingest:file:tests/test_decision_support_gates_v0.py",
    "ingest:file:tests/test_deltas.py",
    "ingest:file:tests/test_demo_auroc_delta.py",
    "ingest:file:tests/test_demo_session.py",
    "ingest:file:tests/test_determinism_guard.py",
    "ingest:file:tests/test_deterministic_mlp.py",
    "ingest:file:tests/test_deterministic_seq_cnn.py",
    "ingest:file:tests/test_divergence_proof_bundle_reader.py",
    "ingest:file:tests/test_divergence.py",
    "ingest:file:tests/test_download_release_contract.py",
    "ingest:file:tests/test_edge_config.py",
    "ingest:file:tests/test_edge_scratch_cleanup.py",
    "ingest:file:tests/test_edit_dag_display_formatting.py",
    "ingest:file:tests/test_edit_dag_frames.py",
    "ingest:file:tests/test_edit_dag_layout_invariants.py",
    "ingest:file:tests/test_edit_dag.py",
    "ingest:file:tests/test_egfr_grb2_mvp.py",
    "ingest:file:tests/test_egfr_grb2_regression.py",
    "ingest:file:tests/test_enterprise_proof_offtarget_public_doc.py",
    "ingest:file:tests/test_enzyme_contract_v1.py",
    "ingest:file:tests/test_eval_azimuth_pack_auroc.py",
    "ingest:file:tests/test_evaluation_pack_v1.py",
    "ingest:file:tests/test_evaluator_docs_loop_contract.py",
    "ingest:file:tests/test_evaluator_mvp_smoke.py",
    "ingest:file:tests/test_evaluator_release_contract.py",
    "ingest:file:tests/test_event_log.py",
    "ingest:file:tests/test_evidence_view_model.py",
    "ingest:file:tests/test_evs/test_offtarget_heat.py",
    "ingest:file:tests/test_experiment_planner.py",
    "ingest:file:tests/test_experiment_presets.py",
    "ingest:file:tests/test_experiment_setup_dialog.py",
    "ingest:file:tests/test_export_evidence.py",
    "ingest:file:tests/test_export_gate_keys.py",
    "ingest:file:tests/test_export_run.py",
    "ingest:file:tests/test_export_verify.py",
    "ingest:file:tests/test_extension_host_heartbeat.py",
    "ingest:file:tests/test_extension_host.py",
    "ingest:file:tests/test_filter_only_ui_no_ranking.py",
    "ingest:file:tests/test_fm_index.py",
    "ingest:file:tests/test_focus_lens_and_physics.py",
    "ingest:file:tests/test_gate_mode_artifact.py",
    "ingest:file:tests/test_gate_mode_golden_fixtures.py",
    "ingest:file:tests/test_gc_homopolymer_cuda.py",
    "ingest:file:tests/test_genome_editing_evidence_runtime.py",
    "ingest:file:tests/test_geom_builders.py",
    "ingest:file:tests/test_geometry_compiler_determinism.py",
    "ingest:file:tests/test_gl_panel_export_clip.py",
    "ingest:file:tests/test_gl_panel.py",
    "ingest:file:tests/test_golden_failing_bundle_v1.py",
    "ingest:file:tests/test_governance_ledger_v1.py",
    "ingest:file:tests/test_governance_no_side_channels_cli.py",
    "ingest:file:tests/test_governance_repo_balance.py",
    "ingest:file:tests/test_governance_self_check_cli.py",
    "ingest:file:tests/test_governance_watermarking.py",
    "ingest:file:tests/test_gpu_l0_thermo.py",
    "ingest:file:tests/test_graphs_colored.py",
    "ingest:file:tests/test_graphs_dbg.py",
    "ingest:file:tests/test_guide_inspector_model.py",
    "ingest:file:tests/test_helix_api.py",
    "ingest:file:tests/test_helix_cli.py",
    "ingest:file:tests/test_helixspec_canon_hash.py",
    "ingest:file:tests/test_helixspec_diff.py",
    "ingest:file:tests/test_helixspec_lower_engine.py",
    "ingest:file:tests/test_helixspec_parse.py",
    "ingest:file:tests/test_helixspec_typecheck.py",
    "ingest:file:tests/test_hero_status.py",
    "ingest:file:tests/test_hostile_bypass_pack_v1.py",
    "ingest:file:tests/test_hub_cli_hub_root_anywhere.py",
    "ingest:file:tests/test_hub_decision_export_v0.py",
    "ingest:file:tests/test_hub_decision_v1.py",
    "ingest:file:tests/test_hub_example_bundle_v1.py",
    "ingest:file:tests/test_hub_pilot_export_v0.py",
    "ingest:file:tests/test_hub_proof_render_v0.py",
    "ingest:file:tests/test_hub_review_v0.py",
    "ingest:file:tests/test_illumina_translator.py",
    "ingest:file:tests/test_importers_ampseq.py",
    "ingest:file:tests/test_importers_bam.py",
    "ingest:file:tests/test_importers_crispresso.py",
    "ingest:file:tests/test_importers_integration_headless.py",
    "ingest:file:tests/test_importers_registry.py",
    "ingest:file:tests/test_importers_to_run_record.py",
    "ingest:file:tests/test_indel_risk_cuda.py",
    "ingest:file:tests/test_ingest_registry_config.py",
    "ingest:file:tests/test_ingest_status_client.py",
    "ingest:file:tests/test_ingest_status_update_api.py",
    "ingest:file:tests/test_ingest_verification.py",
    "ingest:file:tests/test_instrument_runs_view.py",
    "ingest:file:tests/test_intake_ledger.py",
    "ingest:file:tests/test_integration_studio_project_artifacts.py",
    "ingest:file:tests/test_integration_studio_project_workflow.py",
    "ingest:file:tests/test_integration_studio.py",
    "ingest:file:tests/test_invariants.py",
    "ingest:file:tests/test_ion_receiver_cli.py",
    "ingest:file:tests/test_ion_torrent_receiver.py",
    "ingest:file:tests/test_ion_torrent_translator.py",
    "ingest:file:tests/test_iterated_dynamics.py",
    "ingest:file:tests/test_layout_state.py",
    "ingest:file:tests/test_licensing.py",
    "ingest:file:tests/test_lightcone_3d_view_mode.py",
    "ingest:file:tests/test_lightcone_demo_proof_v0_8.py",
    "ingest:file:tests/test_lightcone_drag_threshold.py",
    "ingest:file:tests/test_lightcone_fixture_schema.py",
    "ingest:file:tests/test_lightcone_gpu_parity.py",
    "ingest:file:tests/test_lightcone_gpu_raster_receipts.py",
    "ingest:file:tests/test_lightcone_panel_smoke.py",
    "ingest:file:tests/test_lightcone_perf_profile.py",
    "ingest:file:tests/test_lightcone_perf_smoke.py",
    "ingest:file:tests/test_lightcone_picking.py",
    "ingest:file:tests/test_lightcone_render_golden.py",
    "ingest:file:tests/test_lightcone_stress_tree_determinism.py",
    "ingest:file:tests/test_live_cli.py",
    "ingest:file:tests/test_main_window_placeholders.py",
    "ingest:file:tests/test_metrics_auroc.py",
    "ingest:file:tests/test_metrics_roi.py",
    "ingest:file:tests/test_mock_run_ingest_server.py",
    "ingest:file:tests/test_modern_engine_time_units.py",
    "ingest:file:tests/test_modern_qt_dpi.py",
    "ingest:file:tests/test_modern_qt_dpr_guardrail.py",
    "ingest:file:tests/test_modern_qt_dpr_resize_click_mapping_guardrail.py",
    "ingest:file:tests/test_modern_qt_pick_alloc_separation_guardrail.py",
    "ingest:file:tests/test_modern_qt_picking_mapping.py",
    "ingest:file:tests/test_modern_qt_render_activation.py",
    "ingest:file:tests/test_modern_qt_resize_alloc_guard.py",
    "ingest:file:tests/test_motif.py",
    "ingest:file:tests/test_nussinov.py",
    "ingest:file:tests/test_offtarget_benchmark.py",
    "ingest:file:tests/test_offtarget_cuda_integration.py",
    "ingest:file:tests/test_offtarget_density_cuda.py",
    "ingest:file:tests/test_offtarget_full_determinism.py",
    "ingest:file:tests/test_offtarget_parity.py",
    "ingest:file:tests/test_offtarget_properties.py",
    "ingest:file:tests/test_ogn_gating.py",
    "ingest:file:tests/test_ogn_manager.py",
    "ingest:file:tests/test_ontargetx_bundle_io.py",
    "ingest:file:tests/test_ontargetx_embedding_v3_kmer2.py",
    "ingest:file:tests/test_ontargetx_embedding_v4_kmer3hash256.py",
    "ingest:file:tests/test_ontargetx_embedding_v4_thermo_positional.py",
    "ingest:file:tests/test_ontargetx_embedding_v5_pos1hot.py",
    "ingest:file:tests/test_ontargetx_embedding_v6_kmer2_thermo.py",
    "ingest:file:tests/test_ontargetx_encoding.py",
    "ingest:file:tests/test_ontargetx_engine_bundle.py",
    "ingest:file:tests/test_ontargetx_ensemble_cv.py",
    "ingest:file:tests/test_ontargetx_governance.py",
    "ingest:file:tests/test_ontargetx_ranking_pairs.py",
    "ingest:file:tests/test_open_snapshot_activates_evs.py",
    "ingest:file:tests/test_optional_deps_errors.py",
    "ingest:file:tests/test_outcome_determinism_permutation.py",
    "ingest:file:tests/test_outcome_explorer_mass.py",
    "ingest:file:tests/test_outcome_explorer.py",
    "ingest:file:tests/test_outcome_flow_intent.py",
    "ingest:file:tests/test_outcome_metadata_chips.py",
    "ingest:file:tests/test_outcome_normalize.py",
    "ingest:file:tests/test_outcome_perturbation_cache.py",
    "ingest:file:tests/test_outcome_posterior.py",
    "ingest:file:tests/test_outcome_ribbon_label_selection.py",
    "ingest:file:tests/test_outcome_space_map.py",
    "ingest:file:tests/test_outcome_stale_drop.py",
    "ingest:file:tests/test_packaging_metadata.py",
    "ingest:file:tests/test_packaging_pyinstaller_doc_contract.py",
    "ingest:file:tests/test_packaging_release_contract.py",
    "ingest:file:tests/test_packaging_trusted_release_contract.py",
    "ingest:file:tests/test_pam_seed_cuda.py",
    "ingest:file:tests/test_partner_followup.py",
    "ingest:file:tests/test_pcr_engine.py",
    "ingest:file:tests/test_phase1_knn.py",
    "ingest:file:tests/test_playground_crispr_micro.py",
    "ingest:file:tests/test_plugin_isolation_rules.py",
    "ingest:file:tests/test_plugin_packages.py",
    "ingest:file:tests/test_plugin_registries.py",
    "ingest:file:tests/test_plugin_registry_cache.py",
    "ingest:file:tests/test_plugins_manager.py",
    "ingest:file:tests/test_plugins_manifest.py",
    "ingest:file:tests/test_policy_packs.py",
    "ingest:file:tests/test_policy_patches.py",
    "ingest:file:tests/test_predictor_receipts.py",
    "ingest:file:tests/test_pricing_enforcement_contract.py",
    "ingest:file:tests/test_prime_dp_cuda.py",
    "ingest:file:tests/test_prime_engine.py",
    "ingest:file:tests/test_prime_multiplex_calibration.py",
    "ingest:file:tests/test_prime_physics_score.py",
    "ingest:file:tests/test_prime_physics.py",
    "ingest:file:tests/test_project_imported_runs.py",
    "ingest:file:tests/test_project_model.py",
    "ingest:file:tests/test_project_snapshot_paths.py",
    "ingest:file:tests/test_project_viz_paths.py",
    "ingest:file:tests/test_proof_kit_builder.py",
    "ingest:file:tests/test_protein.py",
    "ingest:file:tests/test_provenance_headers.py",
    "ingest:file:tests/test_provenance_race.py",
    "ingest:file:tests/test_provenance.py",
    "ingest:file:tests/test_public_release_channel_contract.py",
    "ingest:file:tests/test_public_release_docs_contract.py",
    "ingest:file:tests/test_public_validation_packs_v1.py",
    "ingest:file:tests/test_publish_github_release.py",
    "ingest:file:tests/test_publish_website_release.py",
    "ingest:file:tests/test_pypi_publishing_contract.py",
    "ingest:file:tests/test_qt_headless_import.py",
    "ingest:file:tests/test_rail_health_bar_widget.py",
    "ingest:file:tests/test_rail_state_store.py",
    "ingest:file:tests/test_rail_widget_recompute.py",
    "ingest:file:tests/test_rail_widget_spinner_timer.py",
    "ingest:file:tests/test_realtime_transport.py",
    "ingest:file:tests/test_recompute_chain_policy.py",
    "ingest:file:tests/test_recompute_planner.py",
    "ingest:file:tests/test_reference_validation_bundle_builder.py",
    "ingest:file:tests/test_registry_v1_smoke.py",
    "ingest:file:tests/test_release_asset_provenance_contract.py",
    "ingest:file:tests/test_release_checklist_contract.py",
    "ingest:file:tests/test_release_gates_contract.py",
    "ingest:file:tests/test_release_local.py",
    "ingest:file:tests/test_release_provenance_contract.py",
    "ingest:file:tests/test_release_provenance_statement.py",
    "ingest:file:tests/test_repair_pathways.py",
    "ingest:file:tests/test_repro_adversarial.py",
    "ingest:file:tests/test_repro_backend_parity.py",
    "ingest:file:tests/test_repro_bundle.py",
    "ingest:file:tests/test_repro_filesystem_ordering.py",
    "ingest:file:tests/test_repro_manifest_contract.py",
    "ingest:file:tests/test_repro_subprocess_repeat.py",
    "ingest:file:tests/test_results_adapter_indel_profile.py",
    "ingest:file:tests/test_revenue_plan.py",
    "ingest:file:tests/test_rna_mccaskill.py",
    "ingest:file:tests/test_run_activation_propagates_evs.py",
    "ingest:file:tests/test_run_activation_survives_layout_failure.py",
    "ingest:file:tests/test_run_artifact.py",
    "ingest:file:tests/test_run_bundle.py",
    "ingest:file:tests/test_run_compare_auroc_extract.py",
    "ingest:file:tests/test_run_descriptor_schema.py",
    "ingest:file:tests/test_run_history_mv_repro.py",
    "ingest:file:tests/test_run_history.py",
    "ingest:file:tests/test_run_metrics_json_safe.py",
    "ingest:file:tests/test_run_recorded_updates_analysis_outcome_count.py",
    "ingest:file:tests/test_run_registry_api.py",
    "ingest:file:tests/test_run_registry_status.py",
    "ingest:file:tests/test_run_registry.py",
    "ingest:file:tests/test_s3_blob_store.py",
    "ingest:file:tests/test_save_session_report_writes_file.py",
    "ingest:file:tests/test_scc.py",
    "ingest:file:tests/test_scheduler_islands.py",
    "ingest:file:tests/test_schema_manifest.py",
    "ingest:file:tests/test_scientific_contract.py",
    "ingest:file:tests/test_seed.py",
    "ingest:file:tests/test_selection_utils.py",
    "ingest:file:tests/test_session_model.py",
    "ingest:file:tests/test_session_report_engine_info.py",
    "ingest:file:tests/test_session_report_no_chart.py",
    "ingest:file:tests/test_session_report_watermark.py",
    "ingest:file:tests/test_shipped_ontargetx_v7_manifest.py",
    "ingest:file:tests/test_simbuilder_embedded_layout_smoke.py",
    "ingest:file:tests/test_simbuilder_layout_spacing.py",
    "ingest:file:tests/test_sketch.py",
    "ingest:file:tests/test_smoke_package.py",
    "ingest:file:tests/test_snap_ui_parse_size.py",
    "ingest:file:tests/test_snapshot_bundle.py",
    "ingest:file:tests/test_species_core.py",
    "ingest:file:tests/test_spine_end_to_end.py",
    "ingest:file:tests/test_stage_website_release.py",
    "ingest:file:tests/test_string.py",
    "ingest:file:tests/test_structural_risk.py",
    "ingest:file:tests/test_studio_bootstrap.py",
    "ingest:file:tests/test_studio_core_tabs.py",
    "ingest:file:tests/test_studio_entrypoint.py",
    "ingest:file:tests/test_studio_evaluation_access.py",
    "ingest:file:tests/test_studio_evaluation_gate.py",
    "ingest:file:tests/test_studio_export_parity.py",
    "ingest:file:tests/test_studio_left_tabs_visual_artifact.py",
    "ingest:file:tests/test_studio_plugin_host.py",
    "ingest:file:tests/test_studio_responsiveness.py",
    "ingest:file:tests/test_studio_session_helixspec.py",
    "ingest:file:tests/test_summary_contract_v2.py",
    "ingest:file:tests/test_support_bundle.py",
    "ingest:file:tests/test_sweep.py",
    "ingest:file:tests/test_target_picker_drawer.py",
    "ingest:file:tests/test_target_resolution.py",
    "ingest:file:tests/test_teams_audit_export_v1.py",
    "ingest:file:tests/test_teams_backfill_and_telemetry.py",
    "ingest:file:tests/test_teams_cli_bootstrap.py",
    "ingest:file:tests/test_teams_db_backup.py",
    "ingest:file:tests/test_teams_identity_boundary_docs.py",
    "ingest:file:tests/test_teams_metrics.py",
    "ingest:file:tests/test_teams_oidc_auth.py",
    "ingest:file:tests/test_teams_smoke_contract.py",
    "ingest:file:tests/test_teams_telemetry_seats.py",
    "ingest:file:tests/test_teams_token_policy.py",
    "ingest:file:tests/test_teams_v0_smoke.py",
    "ingest:file:tests/test_theme_stylesheet_smoke.py",
    "ingest:file:tests/test_thermo_connect_translator.py",
    "ingest:file:tests/test_triage.py",
    "ingest:file:tests/test_trust_check_cli.py",
    "ingest:file:tests/test_uploader_streaming.py",
    "ingest:file:tests/test_user_config_profiles.py",
    "ingest:file:tests/test_validate_artifacts.py",
    "ingest:file:tests/test_validation_bundle_verify.py",
    "ingest:file:tests/test_validation_negative_controls.py",
    "ingest:file:tests/test_validation_verdict_vectors.py",
    "ingest:file:tests/test_validation_verdict.py",
    "ingest:file:tests/test_veribiota_checks.py",
    "ingest:file:tests/test_veribiota_cli.py",
    "ingest:file:tests/test_veribiota_export.py",
    "ingest:file:tests/test_verify_fuzz_v1.py",
    "ingest:file:tests/test_verify_pilot_package.py",
    "ingest:file:tests/test_verify_reason_code_contract_v1.py",
    "ingest:file:tests/test_verify_release_provenance.py",
    "ingest:file:tests/test_verify_release_signatures.py",
    "ingest:file:tests/test_viewer_perf_hud_smoke.py",
    "ingest:file:tests/test_visual_diff_report.py",
    "ingest:file:tests/test_web_panel_csp.py",
    "ingest:file:tests/test_web_panel_policy.py",
    "ingest:file:tests/test_web_panels_webengine_smoke.py",
    "ingest:file:tests/test_welcome_dialog_smoke.py",
    "ingest:file:tests/test_wetlab_preflight_linter.py",
    "ingest:file:tests/test_wheel_guard_scroll.py",
    "ingest:file:tests/test_workflow_panel_focus_overlay.py",
    "ingest:file:tests/test_workflow_stats.py",
    "ingest:file:tests/test_workflow2p5d_builder.py",
    "ingest:file:tests/test_zip_artifact_determinism.py",
    "ingest:file:tests/tools/test_batch_eval_base_positions_cli.py",
    "ingest:file:tests/tools/test_batch_eval_leaderboard_cli.py",
    "ingest:file:tests/tools/test_cli_session_contract_runner.py",
    "ingest:file:tests/tools/test_demo_regeneration.py",
    "ingest:file:tests/tools/test_monarchic_repo_balance_cli.py",
    "ingest:file:tests/tools/test_prime_multiplex_leaderboard_cli.py",
    "ingest:file:tests/tools/test_prime_multiplex_leaderboard.py",
    "ingest:file:tests/tools/test_qt_runtime_env.py",
    "ingest:file:tests/tools/test_ship_ontargetx_bundle.py",
    "ingest:file:tests/tools/test_train_ontargetx_bundle_azimuth_cli.py",
    "ingest:file:tests/tools/test_train_ontargetx_bundle_azimuth_hparams.py",
    "ingest:file:tests/tools/test_validate_profiles.py",
    "ingest:file:tests/veribiota/crispr_micro.fna",
    "ingest:file:tests/veribiota/gen_crispr_micro.py",
    "ingest:file:tests/veribiota/gen_pcr_micro.py",
    "ingest:file:tests/veribiota/gen_prime_micro.py",
    "ingest:file:tests/veribiota/pcr_config.json",
    "ingest:file:tests/veribiota/pcr_micro.fna",
    "ingest:file:tests/veribiota/pcr_primers.json",
    "ingest:file:tests/veribiota/prime_editor.json",
    "ingest:file:tests/veribiota/prime_micro.fna",
    "ingest:file:tests/veribiota/prime_peg.json",
    "ingest:file:tests/veribiota/README.md",
    "ingest:file:tests/viz/test_alignment_ribbon_spec.py",
    "ingest:file:tests/viz/test_decision_authority_banner_golden.py",
    "ingest:file:tests/viz/test_distance_heatmap_spec.py",
    "ingest:file:tests/viz/test_minimizers_inputs.py",
    "ingest:file:tests/viz/test_minimizers_spec.py",
    "ingest:file:tests/viz/test_modern_helix_base_count.py",
    "ingest:file:tests/viz/test_modern_qt_helix_reference_golden.py",
    "ingest:file:tests/viz/test_modern_qt_hud_golden.py",
    "ingest:file:tests/viz/test_modern_qt_hud_state_machine.py",
    "ingest:file:tests/viz/test_modern_story_motion_dot_sentinel.py",
    "ingest:file:tests/viz/test_motif_logo_spec.py",
    "ingest:file:tests/viz/test_rail_ribbons_spec.py",
    "ingest:file:tests/viz/test_rna_dotplot_shapes.py",
    "ingest:file:tests/viz/test_rna_dotplot_spec.py",
    "ingest:file:tests/viz/test_seed_chain_spec.py",
    "ingest:file:tools/hubverifier-go/internal/c14n/c14n_test.go",
    "ingest:file:tools/shake_test.py",
    "ingest:file:tools/test_env_guard.py",
    "ingest:file:benchmarks/README.md",
    "ingest:file:deliver_workbench/README.md",
    "ingest:file:deploy/helm/helix-teams/README.md",
    "ingest:file:deploy/k8s/README.md",
    "ingest:file:deploy/README.md",
    "ingest:file:deploy/vastai/README.md",
    "ingest:file:design_partner/README.md",
    "ingest:file:design_partner/sessions/README.md",
    "ingest:file:docs/adr/0001-gui-monolith-refactor.md",
    "ingest:file:docs/artifacts.md",
    "ingest:file:docs/assets/viz/alignment-ribbon.json",
    "ingest:file:docs/assets/viz/alignment-ribbon.viz.json",
    "ingest:file:docs/assets/viz/crispr_playground_dag.json",
    "ingest:file:docs/assets/viz/distance-heatmap.json",
    "ingest:file:docs/assets/viz/distance-heatmap.viz.json",
    "ingest:file:docs/assets/viz/minimizers.json",
    "ingest:file:docs/assets/viz/minimizers.viz.json",
    "ingest:file:docs/assets/viz/motif-logo.json",
    "ingest:file:docs/assets/viz/motif-logo.viz.json",
    "ingest:file:docs/assets/viz/pcr_amplicon_dag.json",
    "ingest:file:docs/assets/viz/prime_playground_dag.json",
    "ingest:file:docs/assets/viz/rna-dotplot.json",
    "ingest:file:docs/assets/viz/rna-dotplot.viz.json",
    "ingest:file:docs/assets/viz/seed-chain.json",
    "ingest:file:docs/assets/viz/seed-chain.viz.json",
    "ingest:file:docs/audit_walkthrough.md",
    "ingest:file:docs/battlecards/benchling.md",
    "ingest:file:docs/benchmarks.md",
    "ingest:file:docs/billion_dollar_thesis.md",
    "ingest:file:docs/ci/verify_gate_template.md",
    "ingest:file:docs/ci/verify_reason_codes.md",
    "ingest:file:docs/cli_config_schema.md",
    "ingest:file:docs/cli_headless.md",
    "ingest:file:docs/cli.md",
    "ingest:file:docs/cli/alpha.md",
    "ingest:file:docs/cli/demo.md",
    "ingest:file:docs/cli/live.md",
    "ingest:file:docs/cli/pcr.md",
    "ingest:file:docs/cli/schema.md",
    "ingest:file:docs/cli/session_contract_v1.md",
    "ingest:file:docs/cli/session_contract_v2.md",
    "ingest:file:docs/cli/session_contract_v3.md",
    "ingest:file:docs/cli/viz.md",
    "ingest:file:docs/cli/workflows.md",
    "ingest:file:docs/competitive_landscape.md",
    "ingest:file:docs/concepts/artifacts.md",
    "ingest:file:docs/concepts/multiscale.md",
    "ingest:file:docs/concepts/outcome_digital_twin.md",
    "ingest:file:docs/concepts/perfection.md",
    "ingest:file:docs/concepts/schemas.md",
    "ingest:file:docs/concepts/workflows.md",
    "ingest:file:docs/contracts/enzyme_program_contract_v1.md",
    "ingest:file:docs/contracts/helix_1_0.md",
    "ingest:file:docs/contracts/lightcone_visual_contract_v0_8.md",
    "ingest:file:docs/contributing.md",
    "ingest:file:docs/crispr_ctmc_tau_leap.md",
    "ingest:file:docs/CROSS_HOST_PROTOCOL.md",
    "ingest:file:docs/decision_cockpit_demo.md",
    "ingest:file:docs/decision_support/spec_v0.md",
    "ingest:file:docs/design_partner_email_template.md",
    "ingest:file:docs/design_partner_program.md",
    "ingest:file:docs/dev_gpu_profiling.md",
    "ingest:file:docs/dev/ci_policy.md",
    "ingest:file:docs/dev/evs.md",
    "ingest:file:docs/dev/offtarget_heat.md",
    "ingest:file:docs/dev/packaging_pyinstaller.md",
    "ingest:file:docs/dev/renderer_fields.md",
    "ingest:file:docs/dev/SECURITY_HARDENING.md",
    "ingest:file:docs/dev/SECURITY_SCANNING.md",
    "ingest:file:docs/dev/ui.md",
    "ingest:file:docs/download.md",
    "ingest:file:docs/edit_dag_frames.md",
    "ingest:file:docs/edit_dag_overview.md",
    "ingest:file:docs/edit-dag-viz.md",
    "ingest:file:docs/engine_architecture.md",
    "ingest:file:docs/engine_cuda_plan.md",
    "ingest:file:docs/enterprise_proof/auroc_delta_demo.md",
    "ingest:file:docs/enterprise_proof/azimuth_public.md",
    "ingest:file:docs/enterprise_proof/evaluation_guide.md",
    "ingest:file:docs/enterprise_proof/government-ready-product-surface.md",
    "ingest:file:docs/enterprise_proof/index.md",
    "ingest:file:docs/enterprise_proof/offtarget_public.md",
    "ingest:file:docs/enterprise_proof/roi.md",
    "ingest:file:docs/enterprise_proof/support_policy.md",
    "ingest:file:docs/enterprise_proof/teams_deploy_guide.md",
    "ingest:file:docs/evs_visual_tests.md",
    "ingest:file:docs/evs_visual.md",
    "ingest:file:docs/faq_v0_1.md",
    "ingest:file:docs/features_catalog.md",
    "ingest:file:docs/genome_editing_evidence_runtime_v0_1.md",
    "ingest:file:docs/getting-started.md",
    "ingest:file:docs/governance_contract.md",
    "ingest:file:docs/governed_predictor_adapters.md",
    "ingest:file:docs/helix_experiment_roadmap.md",
    "ingest:file:docs/helix_principles.md",
    "ingest:file:docs/helixspec_mvp.md",
    "ingest:file:docs/helixspec_quickstart.md",
    "ingest:file:docs/hub/end_to_end_v0.md",
    "ingest:file:docs/hub/example_bundle.md",
    "ingest:file:docs/hub/index.md",
    "ingest:file:docs/hub/investor_memo.md",
    "ingest:file:docs/hub/pilot.md",
    "ingest:file:docs/hub/pitch.md",
    "ingest:file:docs/hub/proof_url_v0.md",
    "ingest:file:docs/hub/review_v0.md",
    "ingest:file:docs/hub/rfcs/index.md",
    "ingest:file:docs/hub/rfcs/rfc_0001_bundle_spec_v1.md",
    "ingest:file:docs/hub/rfcs/rfc_0002_canonical_json_v1.md",
    "ingest:file:docs/hub/rfcs/rfc_0003_run_receipt_v1.md",
    "ingest:file:docs/hub/rfcs/rfc_0004_approval_surface_v1.md",
    "ingest:file:docs/hub/rfcs/rfc_0005_approval_receipt_v1.md",
    "ingest:file:docs/hub/rfcs/rfc_0006_audit_export_v1.md",
    "ingest:file:docs/hub/rfcs/rfc_0007_job_v1.md",
    "ingest:file:docs/hub/rfcs/rfc_0008_backend_fingerprint_v1.md",
    "ingest:file:docs/hub/rfcs/rfc_0009_decision_v1.md",
    "ingest:file:docs/hub/trust_model.md",
    "ingest:file:docs/index.md",
    "ingest:file:docs/instructions.md",
    "ingest:file:docs/lightcone_v0_9_milestone.md",
    "ingest:file:docs/model_limitations/crispr_edit_dag_limitations.md",
    "ingest:file:docs/never_do.md",
    "ingest:file:docs/non_goals.md",
    "ingest:file:docs/notebooks/edit_dag_visual_demo.ipynb",
    "ingest:file:docs/ogn_integration.md",
    "ingest:file:docs/omnis_helix_screenshots.md",
    "ingest:file:docs/omnis_helix_strategy.md",
    "ingest:file:docs/omnis_helix_tour.md",
    "ingest:file:docs/paper_deterministic_genome_editing.md",
    "ingest:file:docs/partner_intake.md",
    "ingest:file:docs/partner_ops_playbook.md",
    "ingest:file:docs/playground/index.html",
    "ingest:file:docs/playground/js/realtime_branch_chart.js",
    "ingest:file:docs/playground/js/realtime_compare.js",
    "ingest:file:docs/playground/js/realtime_worker.js",
    "ingest:file:docs/playground/js/realtime.js",
    "ingest:file:docs/playground/realtime.html",
    "ingest:file:docs/policies/compatibility_deprecation.md",
    "ingest:file:docs/policies/conformance.md",
    "ingest:file:docs/policies/export_governance.md",
    "ingest:file:docs/policies/external_attestation.md",
    "ingest:file:docs/policies/governance_registry_policy.md",
    "ingest:file:docs/policies/incident_playbook.md",
    "ingest:file:docs/policies/lean_bridge.md",
    "ingest:file:docs/policies/longevity.md",
    "ingest:file:docs/policies/observability.md",
    "ingest:file:docs/policies/off_target_constraint.md",
    "ingest:file:docs/policies/performance_contracts.md",
    "ingest:file:docs/policies/plugin_governance.md",
    "ingest:file:docs/policies/policy_controls.md",
    "ingest:file:docs/policies/release_provenance.md",
    "ingest:file:docs/policies/schema_hygiene.md",
    "ingest:file:docs/policies/security.md",
    "ingest:file:docs/policies/semantic_drift.md",
    "ingest:file:docs/policies/ux_onboarding.md",
    "ingest:file:docs/positioning.md",
    "ingest:file:docs/prime_physics.md",
    "ingest:file:docs/product_manual.md",
    "ingest:file:docs/proof_bundles.md",
    "ingest:file:docs/proofs/lightcone_demo_proof_v0_8.md",
    "ingest:file:docs/public_release_channel.md",
    "ingest:file:docs/pypi_publishing.md",
    "ingest:file:docs/rail_control_plane.md",
    "ingest:file:docs/reference_validation_bundle.md",
    "ingest:file:docs/reference/api.md",
    "ingest:file:docs/release_checklist.md",
    "ingest:file:docs/RELEASE_VERIFY.md",
    "ingest:file:docs/repo_audit_1b_thesis.json",
    "ingest:file:docs/repo_audit_1b_thesis.md",
    "ingest:file:docs/run_graph.md",
    "ingest:file:docs/run_ingest.md",
    "ingest:file:docs/runbooks/knockout_decision_gate_demo.md",
    "ingest:file:docs/runbooks/lightcone_runbook.md",
    "ingest:file:docs/schema-reference.md",
    "ingest:file:docs/schema.md",
    "ingest:file:docs/scientific_contract_v1.md",
    "ingest:file:docs/scoring_version.md",
    "ingest:file:docs/snapshot_spec_v1.md",
    "ingest:file:docs/snapshot_spec_v1.schema.json",
    "ingest:file:docs/studio/core_features.md",
    "ingest:file:docs/studio/plugins.md",
    "ingest:file:docs/switching_proof_excerpt.txt",
    "ingest:file:docs/switching_proof.md",
    "ingest:file:docs/teams_v0.md",
    "ingest:file:docs/threat_model.md",
    "ingest:file:docs/trust_kit.md",
    "ingest:file:docs/v0_5_milestone.md",
    "ingest:file:docs/validation_crispr_efficiency_panel.md",
    "ingest:file:docs/validation_crispr_offtarget_panel.md",
    "ingest:file:docs/validation_crispr_plasmid.md",
    "ingest:file:docs/validation_prime_panel.md",
    "ingest:file:docs/validation/README.md",
    "ingest:file:docs/veribiota.md",
    "ingest:file:docs/visualization/alignment-ribbon.md",
    "ingest:file:docs/visualization/distance-heatmap.md",
    "ingest:file:docs/visualization/minimizer-density.md",
    "ingest:file:docs/visualization/motif-logo.md",
    "ingest:file:docs/visualization/rna-dotplot.md",
    "ingest:file:docs/viz.md",
    "ingest:file:docs/wetlab_preflight_linter.md",
    "ingest:file:docs/whats-new.md",
    "ingest:file:docs/why_helix.md",
    "ingest:file:examples/delivery/README.md",
    "ingest:file:examples/offscreen_webrtc_demo/README_hw.md",
    "ingest:file:examples/offscreen_webrtc_demo/README.md",
    "ingest:file:examples/plugins/hello_world/README.md",
    "ingest:file:examples/plugins/remote_echo/README.md",
    "ingest:file:examples/plugins/remote_web_panel/README.md",
    "ingest:file:examples/proof/helix_editing_decisions_v1/README.md",
    "ingest:file:examples/README.md",
    "ingest:file:experiments/infrastructure_validation_suite/multi_site_reproducibility/README.md",
    "ingest:file:experiments/infrastructure_validation_suite/procurement_bundles/HELIX_IVS_PROCUREMENT_1.0.0_20260212_173410/README.md",
    "ingest:file:experiments/infrastructure_validation_suite/README.md",
    "ingest:file:experiments/README.md",
    "ingest:file:fixtures/golden_failing_bundle_v1/README.md",
    "ingest:file:fixtures/hostile_bypass_pack_v1/README.md",
    "ingest:file:outreach/README.md",
    "ingest:file:README.md",
    "ingest:file:repro/enzyme_contract_v1/README.md",
    "ingest:file:repro/helix_repro_bundle_v1/README.md",
    "ingest:file:repro/scientific_contract_v1/README.md",
    "ingest:file:schemas/evidence/README.md",
    "ingest:file:schemas/run/README.md",
    "ingest:file:schemas/species/README.md",
    "ingest:file:src/helix/campaigns/README.md",
    "ingest:file:src/helix/compute/README.md",
    "ingest:file:src/helix/datasets/evaluation_packs/helix_eval_v1_azimuth_public/README.md",
    "ingest:file:src/helix/datasets/evaluation_packs/helix_eval_v1_batch_demo/README.md",
    "ingest:file:src/helix/datasets/evaluation_packs/helix_eval_v1_offtarget_public_rloks_sensitive/README.md",
    "ingest:file:src/helix/datasets/evaluation_packs/helix_eval_v1_offtarget_public/README.md",
    "ingest:file:src/helix/datasets/validation_packs/ampseq_indel_profile_v1/README.md",
    "ingest:file:src/helix/datasets/validation_packs/bam_qc_coverage_v1/README.md",
    "ingest:file:src/helix/datasets/validation_packs/cas9_nhej_outcome_prediction_v1/README.md",
    "ingest:file:src/helix/datasets/validation_packs/crisprresso_import_v1/README.md",
    "ingest:file:src/helix/datasets/validation_packs/repro_bundle_v1/README.md",
    "ingest:file:src/helix/datasets/validation_packs/signed_plugin_trust_chain_v1/README.md",
    "ingest:file:src/helix/datasets/validation_packs/vcf_qc_annot_v1/README.md",
    "ingest:file:src/helix/studio/experimental/run_history_mv/README.md",
    "ingest:file:tools/hubverifier-go/README.md",
    "ingest:file:Visualization_Bench/README.md",
    "component:requirements-dev.txt",
    "ingest:file:engine/src/helix/cuda/fields/composite_editability.cu",
    "ingest:file:engine/src/helix/cuda/fields/dcas9_occupancy.cu",
    "ingest:file:engine/src/helix/cuda/fields/gc_homopolymer.cu",
    "ingest:file:engine/src/helix/cuda/fields/indel_risk.cu",
    "ingest:file:engine/src/helix/cuda/fields/offtarget_density.cu",
    "ingest:file:engine/src/helix/cuda/fields/pam_seed.cu",
    "ingest:file:engine/src/helix/cuda/fields/prime_dp.cu",
    "ingest:file:src/helix_engine/src/binding.cpp",
    "ingest:file:src/helix_engine/src/ctmc_tau_leap_cuda.cu",
    "ingest:file:src/helix_engine/src/l0_thermo.cu",
    "ingest:file:src/helix_engine/src/physics_cuda.cu",
    "ingest:file:src/helix_engine/src/physics.cpp",
    "ingest:file:src/helix_engine/src/sha256.cpp"
  ],
  "qualityWarnings": []
}

</details>

Helix Wiki

Purpose: Helix is a repository indexed by RepoIntel MCP.

Documentation starts at benchmarks/README.md, deliver_workbench/README.md, deploy/helm/helix-teams/README.md.

Context:

• Version control: git
• Detected ecosystems: go, node, python
• Inventory: 2706 files, 134 components, 8 workflows

Related Pages

• architecture
• configuration
• playbook
• validation
• change-guide
• troubleshooting
• dependencies
• workflows
• components
• diagrams
• interfaces
• testing
• glossary

Repository Overview

Purpose: Helix is a repository indexed by RepoIntel MCP.

Documentation starts at benchmarks/README.md, deliver_workbench/README.md, deploy/helm/helix-teams/README.md.

Context:

• Version control: git
• Detected ecosystems: go, node, python
• Inventory: 2706 files, 134 components, 8 workflows

Primary capabilities:

• build: make
• run: helix
• run: helix-campaign
• run: helix-cli

Major subsystem map:

• external: external groups 118 components under external/ or related paths.
• root: root groups 9 components under root/ or related paths.
• src: src groups 4 components using path structure plus graph-connected merges.
• tools: tools groups 2 components under tools/ or related paths.

Suggested reading order:

1. Read Architecture next for the subsystem view.
2. Read Configuration next for the required setup, tunable knobs, and risk-sensitive settings.
3. Read Playbook next for the operational validation and debugging guide.
4. Read Validation next for the validation layers and the confidence they provide.
5. Read Change Guide next for the task-first change priorities, edit entrypoints, and verification order.
6. Read Troubleshooting next for the failure-first inspection points and validation commands.
7. Read Dependencies next for the dependencies details.
8. Read Workflows next for the workflows details.
9. Read Components next for the important component inventory.
10. Read Diagrams next for the diagrams details.
11. Read Interfaces next for the interfaces details.
12. Read Testing next for the testing details.
13. Read Glossary next for the glossary details.

<details> <summary>Related files:</summary>

• benchmarks/README.md
• deliver_workbench/README.md
• deploy/helm/helix-teams/README.md
• deploy/k8s/README.md
• deploy/README.md
• deploy/vastai/README.md
• design_partner/README.md
• design_partner/sessions/README.md
• examples/offscreen_webrtc_demo/signaling/package.json
• examples/offscreen_webrtc_demo/signaling/server.js
• tools/hubverifier-go/cmd/hubverify/main.go
• tools/hubverifier-go/go.mod
• engine/src/helix/cuda/fields/composite_editability.cu
• engine/src/helix/cuda/fields/dcas9_occupancy.cu

</details> <details> <summary>Citations:</summary>

• benchmarks/README.md
• deliver_workbench/README.md
• deploy/helm/helix-teams/README.md
• deploy/k8s/README.md
• deploy/README.md
• deploy/vastai/README.md
• examples/offscreen_webrtc_demo/signaling/package.json
• examples/offscreen_webrtc_demo/signaling/server.js:6
• tools/hubverifier-go/cmd/hubverify/main.go:22
• tools/hubverifier-go/go.mod
• engine/src/helix/cuda/fields/composite_editability.cu
• engine/src/helix/cuda/fields/dcas9_occupancy.cu

</details>

Critical Components

1. src

Why it matters: Hotspot score 93609 with 16933 inbound and 14267 outbound inferred edges. Owns 19 interface or config surfaces. Touches 2177 inferred dependency edges.

What it owns:

• Source module rooted at src.
• Owns files rooted at src.

<details> <summary>Supporting citations:</summary>

• src/helix_api.py
• src/helix_cuda_fields.py
• src/helix_engine/__init__.py

</details>

Ranking score: 95843.

2. Tests

Why it matters: Hotspot score 33501 with 2194 inbound and 8970 outbound inferred edges. Touches 1552 inferred dependency edges.

What it owns:

• Repository tests and fixtures.
• Owns files rooted at tests.

<details> <summary>Supporting citations:</summary>

• deliver_workbench/tests/__init__.py
• deliver_workbench/tests/test_adapter_e2e.py:16
• deliver_workbench/tests/test_database.py:25

</details>

Ranking score: 35053.

3. helix-governance

Why it matters: Hotspot score 9432 with 3143 inbound and 0 outbound inferred edges. Shows up in 8 inferred workflows.

What it owns:

• helix-governance python component
• Owns root-level repository responsibilities.

<details> <summary>Supporting citations:</summary>

• pyproject.toml
• src/helix_api.py
• src/helix_cuda_fields.py

</details>

Ranking score: 9450.

4. Documentation

Why it matters: Hotspot score 1713 with 491 inbound and 78 outbound inferred edges. Owns 1 interface or config surface. Shows up in 8 inferred workflows.

What it owns:

• Repository documentation and wiki source files.
• Owns root-level repository responsibilities.

<details> <summary>Supporting citations:</summary>

• benchmarks/README.md
• deliver_workbench/README.md
• deploy/helm/helix-teams/README.md

</details>

Ranking score: 1732.

<details> <summary>Related files:</summary>

• src/helix_api.py
• src/helix_cuda_fields.py
• src/helix_engine/__init__.py
• src/helix_engine/CMakeLists.txt
• deliver_workbench/tests/__init__.py
• deliver_workbench/tests/test_adapter_e2e.py
• deliver_workbench/tests/test_database.py
• deliver_workbench/tests/test_matchmaker.py
• pyproject.toml
• benchmarks/README.md
• deliver_workbench/README.md
• deploy/helm/helix-teams/README.md
• deploy/k8s/README.md

</details> <details> <summary>Citations:</summary>

• src/helix_api.py
• src/helix_cuda_fields.py
• src/helix_engine/__init__.py
• deliver_workbench/tests/__init__.py
• deliver_workbench/tests/test_adapter_e2e.py:16
• deliver_workbench/tests/test_database.py:25
• pyproject.toml
• benchmarks/README.md
• deliver_workbench/README.md
• deploy/helm/helix-teams/README.md

</details>

Repository Summary

Purpose: Helix is a repository indexed by RepoIntel MCP.

Documentation starts at benchmarks/README.md, deliver_workbench/README.md, deploy/helm/helix-teams/README.md.

Context:

• Version control: git
• Detected ecosystems: go, node, python
• Inventory: 2706 files, 134 components, 8 workflows

Indexed revision: git:356eed058c9f1734f0f37b94436343ae14cd6c8a. Indexed at: 2026-07-06T00:23:36.995Z.

<details> <summary>Related files:</summary>

• benchmarks/README.md
• deliver_workbench/README.md
• deploy/helm/helix-teams/README.md
• deploy/k8s/README.md
• deploy/README.md
• deploy/vastai/README.md
• design_partner/README.md
• design_partner/sessions/README.md
• docs/adr/0001-gui-monolith-refactor.md
• docs/artifacts.md
• docs/assets/viz/alignment-ribbon.json
• docs/assets/viz/alignment-ribbon.viz.json
• docs/assets/viz/crispr_playground_dag.json
• docs/assets/viz/distance-heatmap.json
• docs/assets/viz/distance-heatmap.viz.json
• docs/assets/viz/minimizers.json
• docs/assets/viz/minimizers.viz.json
• docs/assets/viz/motif-logo.json
• docs/assets/viz/motif-logo.viz.json
• docs/assets/viz/pcr_amplicon_dag.json
• docs/assets/viz/prime_playground_dag.json
• docs/assets/viz/rna-dotplot.json
• docs/assets/viz/rna-dotplot.viz.json
• docs/assets/viz/seed-chain.json
• docs/assets/viz/seed-chain.viz.json
• docs/audit_walkthrough.md
• docs/battlecards/benchling.md
• docs/benchmarks.md
• docs/billion_dollar_thesis.md
• docs/ci/verify_gate_template.md
• docs/ci/verify_reason_codes.md
• docs/cli_config_schema.md
• docs/cli_headless.md
• docs/cli.md
• docs/cli/alpha.md
• docs/cli/demo.md
• docs/cli/live.md
• docs/cli/pcr.md
• docs/cli/schema.md
• docs/cli/session_contract_v1.md
• docs/cli/session_contract_v2.md
• docs/cli/session_contract_v3.md
• docs/cli/viz.md
• docs/cli/workflows.md
• docs/competitive_landscape.md
• docs/concepts/artifacts.md
• docs/concepts/multiscale.md
• docs/concepts/outcome_digital_twin.md
• docs/concepts/perfection.md
• docs/concepts/schemas.md
• docs/concepts/workflows.md
• docs/contracts/enzyme_program_contract_v1.md
• docs/contracts/helix_1_0.md
• docs/contracts/lightcone_visual_contract_v0_8.md
• docs/contributing.md
• docs/crispr_ctmc_tau_leap.md
• docs/CROSS_HOST_PROTOCOL.md
• docs/decision_cockpit_demo.md
• docs/decision_support/spec_v0.md
• docs/design_partner_email_template.md
• docs/design_partner_program.md
• docs/dev_gpu_profiling.md
• docs/dev/ci_policy.md
• docs/dev/evs.md
• docs/dev/offtarget_heat.md
• docs/dev/packaging_pyinstaller.md
• docs/dev/renderer_fields.md
• docs/dev/SECURITY_HARDENING.md
• docs/dev/SECURITY_SCANNING.md
• docs/dev/ui.md
• docs/download.md
• docs/edit_dag_frames.md
• docs/edit_dag_overview.md
• docs/edit-dag-viz.md
• docs/engine_architecture.md
• docs/engine_cuda_plan.md
• docs/enterprise_proof/auroc_delta_demo.md
• docs/enterprise_proof/azimuth_public.md
• docs/enterprise_proof/evaluation_guide.md
• docs/enterprise_proof/government-ready-product-surface.md
• docs/enterprise_proof/index.md
• docs/enterprise_proof/offtarget_public.md
• docs/enterprise_proof/roi.md
• docs/enterprise_proof/support_policy.md
• docs/enterprise_proof/teams_deploy_guide.md
• docs/evs_visual_tests.md
• docs/evs_visual.md
• docs/faq_v0_1.md
• docs/features_catalog.md
• docs/genome_editing_evidence_runtime_v0_1.md
• docs/getting-started.md
• docs/governance_contract.md
• docs/governed_predictor_adapters.md
• docs/helix_experiment_roadmap.md
• docs/helix_principles.md
• docs/helixspec_mvp.md
• docs/helixspec_quickstart.md
• docs/hub/end_to_end_v0.md
• docs/hub/example_bundle.md
• docs/hub/index.md
• docs/hub/investor_memo.md
• docs/hub/pilot.md
• docs/hub/pitch.md
• docs/hub/proof_url_v0.md
• docs/hub/review_v0.md
• docs/hub/rfcs/index.md
• docs/hub/rfcs/rfc_0001_bundle_spec_v1.md
• docs/hub/rfcs/rfc_0002_canonical_json_v1.md
• docs/hub/rfcs/rfc_0003_run_receipt_v1.md
• docs/hub/rfcs/rfc_0004_approval_surface_v1.md
• docs/hub/rfcs/rfc_0005_approval_receipt_v1.md
• docs/hub/rfcs/rfc_0006_audit_export_v1.md
• docs/hub/rfcs/rfc_0007_job_v1.md
• docs/hub/rfcs/rfc_0008_backend_fingerprint_v1.md
• docs/hub/rfcs/rfc_0009_decision_v1.md
• docs/hub/trust_model.md
• docs/index.md
• docs/instructions.md
• docs/lightcone_v0_9_milestone.md
• docs/model_limitations/crispr_edit_dag_limitations.md
• docs/never_do.md
• docs/non_goals.md
• docs/notebooks/edit_dag_visual_demo.ipynb
• docs/ogn_integration.md
• docs/omnis_helix_screenshots.md
• docs/omnis_helix_strategy.md
• docs/omnis_helix_tour.md
• docs/paper_deterministic_genome_editing.md
• docs/partner_intake.md
• docs/partner_ops_playbook.md
• docs/playground/index.html
• docs/playground/js/realtime_branch_chart.js
• docs/playground/js/realtime_compare.js
• docs/playground/js/realtime_worker.js
• docs/playground/js/realtime.js
• docs/playground/realtime.html
• docs/policies/compatibility_deprecation.md
• docs/policies/conformance.md
• docs/policies/export_governance.md
• docs/policies/external_attestation.md
• docs/policies/governance_registry_policy.md
• docs/policies/incident_playbook.md
• docs/policies/lean_bridge.md
• docs/policies/longevity.md
• docs/policies/observability.md
• docs/policies/off_target_constraint.md
• docs/policies/performance_contracts.md
• docs/policies/plugin_governance.md
• docs/policies/policy_controls.md
• docs/policies/release_provenance.md
• docs/policies/schema_hygiene.md
• docs/policies/security.md
• docs/policies/semantic_drift.md
• docs/policies/ux_onboarding.md
• docs/positioning.md
• docs/prime_physics.md
• docs/product_manual.md
• docs/proof_bundles.md
• docs/proofs/lightcone_demo_proof_v0_8.md
• docs/public_release_channel.md
• docs/pypi_publishing.md
• docs/rail_control_plane.md
• docs/reference_validation_bundle.md
• docs/reference/api.md
• docs/release_checklist.md
• docs/RELEASE_VERIFY.md
• docs/repo_audit_1b_thesis.json
• docs/repo_audit_1b_thesis.md
• docs/run_graph.md
• docs/run_ingest.md
• docs/runbooks/knockout_decision_gate_demo.md
• docs/runbooks/lightcone_runbook.md
• docs/schema-reference.md
• docs/schema.md
• docs/scientific_contract_v1.md
• docs/scoring_version.md
• docs/snapshot_spec_v1.md
• docs/snapshot_spec_v1.schema.json
• docs/studio/core_features.md
• docs/studio/plugins.md
• docs/switching_proof_excerpt.txt
• docs/switching_proof.md
• docs/teams_v0.md
• docs/threat_model.md
• docs/trust_kit.md
• docs/v0_5_milestone.md
• docs/validation_crispr_efficiency_panel.md
• docs/validation_crispr_offtarget_panel.md
• docs/validation_crispr_plasmid.md
• docs/validation_prime_panel.md
• docs/validation/README.md
• docs/veribiota.md
• docs/visualization/alignment-ribbon.md
• docs/visualization/distance-heatmap.md
• docs/visualization/minimizer-density.md
• docs/visualization/motif-logo.md
• docs/visualization/rna-dotplot.md
• docs/viz.md
• docs/wetlab_preflight_linter.md
• docs/whats-new.md
• docs/why_helix.md
• examples/delivery/README.md
• examples/offscreen_webrtc_demo/README_hw.md
• examples/offscreen_webrtc_demo/README.md
• examples/plugins/hello_world/README.md
• examples/plugins/remote_echo/README.md
• examples/plugins/remote_web_panel/README.md
• examples/proof/helix_editing_decisions_v1/README.md
• examples/README.md
• experiments/infrastructure_validation_suite/multi_site_reproducibility/README.md
• experiments/infrastructure_validation_suite/procurement_bundles/HELIX_IVS_PROCUREMENT_1.0.0_20260212_173410/README.md
• experiments/infrastructure_validation_suite/README.md
• experiments/README.md
• fixtures/golden_failing_bundle_v1/README.md
• fixtures/hostile_bypass_pack_v1/README.md
• outreach/README.md
• README.md
• repro/enzyme_contract_v1/README.md
• repro/helix_repro_bundle_v1/README.md
• repro/scientific_contract_v1/README.md
• schemas/evidence/README.md
• schemas/run/README.md
• schemas/species/README.md
• src/helix/campaigns/README.md
• src/helix/compute/README.md
• src/helix/datasets/evaluation_packs/helix_eval_v1_azimuth_public/README.md
• src/helix/datasets/evaluation_packs/helix_eval_v1_batch_demo/README.md
• src/helix/datasets/evaluation_packs/helix_eval_v1_offtarget_public_rloks_sensitive/README.md
• src/helix/datasets/evaluation_packs/helix_eval_v1_offtarget_public/README.md
• src/helix/datasets/validation_packs/ampseq_indel_profile_v1/README.md
• src/helix/datasets/validation_packs/bam_qc_coverage_v1/README.md
• src/helix/datasets/validation_packs/cas9_nhej_outcome_prediction_v1/README.md
• src/helix/datasets/validation_packs/crisprresso_import_v1/README.md
• src/helix/datasets/validation_packs/repro_bundle_v1/README.md
• src/helix/datasets/validation_packs/signed_plugin_trust_chain_v1/README.md
• src/helix/datasets/validation_packs/vcf_qc_annot_v1/README.md
• src/helix/studio/experimental/run_history_mv/README.md
• tests/fixtures/lightcone/README.md
• tests/systems/fixtures/benchmark_panel/README.md
• tests/veribiota/README.md
• tools/hubverifier-go/README.md
• Visualization_Bench/README.md

</details> <details> <summary>Citations:</summary>

• benchmarks/README.md
• deliver_workbench/README.md
• deploy/helm/helix-teams/README.md
• deploy/k8s/README.md
• deploy/README.md
• deploy/vastai/README.md
• design_partner/README.md
• design_partner/sessions/README.md
• docs/adr/0001-gui-monolith-refactor.md
• docs/artifacts.md

</details>

Repository Shape

• .bench/
• .githooks/
• .github/
• .helix/
• .playwright-mcp/
• .repointel/
• .smoke_systems/
• VeriBiota/
• Visualization_Bench/
• baselines/
• benchmarks/
• calibration/
• deliver_workbench/
• deploy/
• design_partner/
• docs/
• engine/
• examples/
• experiments/
• fixtures/
• helix/
• helix_gui/
• helixtasks/
• keys/
• live_runs/
• notebooks/
• out/
• outreach/
• packaging/
• policies/
• python/
• repro/
• schemas/
• scripts/
• shaders/
• src/
• state/
• stdlib/
• templates/
• tests/
• tools/
• veribiota_work/
• viz_transforms/
• workflows/

Languages:

• go
• javascript
• json
• markdown
• python
• shell
• toml
• yaml

<details> <summary>Related files:</summary>

• benchmarks/README.md
• deliver_workbench/README.md
• deploy/helm/helix-teams/README.md
• deploy/k8s/README.md
• deploy/README.md
• deploy/vastai/README.md
• design_partner/README.md
• design_partner/sessions/README.md
• docs/adr/0001-gui-monolith-refactor.md
• docs/artifacts.md
• docs/assets/viz/alignment-ribbon.json
• docs/assets/viz/alignment-ribbon.viz.json
• docs/assets/viz/crispr_playground_dag.json
• docs/assets/viz/distance-heatmap.json
• docs/assets/viz/distance-heatmap.viz.json
• docs/assets/viz/minimizers.json
• docs/assets/viz/minimizers.viz.json
• docs/assets/viz/motif-logo.json
• docs/assets/viz/motif-logo.viz.json
• docs/assets/viz/pcr_amplicon_dag.json
• docs/assets/viz/prime_playground_dag.json
• docs/assets/viz/rna-dotplot.json
• docs/assets/viz/rna-dotplot.viz.json
• docs/assets/viz/seed-chain.json
• docs/assets/viz/seed-chain.viz.json
• docs/audit_walkthrough.md
• docs/battlecards/benchling.md
• docs/benchmarks.md
• docs/billion_dollar_thesis.md
• docs/ci/verify_gate_template.md
• docs/ci/verify_reason_codes.md
• docs/cli_config_schema.md
• docs/cli_headless.md
• docs/cli.md
• docs/cli/alpha.md
• docs/cli/demo.md
• docs/cli/live.md
• docs/cli/pcr.md
• docs/cli/schema.md
• docs/cli/session_contract_v1.md
• docs/cli/session_contract_v2.md
• docs/cli/session_contract_v3.md
• docs/cli/viz.md
• docs/cli/workflows.md
• docs/competitive_landscape.md
• docs/concepts/artifacts.md
• docs/concepts/multiscale.md
• docs/concepts/outcome_digital_twin.md
• docs/concepts/perfection.md
• docs/concepts/schemas.md
• docs/concepts/workflows.md
• docs/contracts/enzyme_program_contract_v1.md
• docs/contracts/helix_1_0.md
• docs/contracts/lightcone_visual_contract_v0_8.md
• docs/contributing.md
• docs/crispr_ctmc_tau_leap.md
• docs/CROSS_HOST_PROTOCOL.md
• docs/decision_cockpit_demo.md
• docs/decision_support/spec_v0.md
• docs/design_partner_email_template.md
• docs/design_partner_program.md
• docs/dev_gpu_profiling.md
• docs/dev/ci_policy.md
• docs/dev/evs.md
• docs/dev/offtarget_heat.md
• docs/dev/packaging_pyinstaller.md
• docs/dev/renderer_fields.md
• docs/dev/SECURITY_HARDENING.md
• docs/dev/SECURITY_SCANNING.md
• docs/dev/ui.md
• docs/download.md
• docs/edit_dag_frames.md
• docs/edit_dag_overview.md
• docs/edit-dag-viz.md
• docs/engine_architecture.md
• docs/engine_cuda_plan.md
• docs/enterprise_proof/auroc_delta_demo.md
• docs/enterprise_proof/azimuth_public.md
• docs/enterprise_proof/evaluation_guide.md
• docs/enterprise_proof/government-ready-product-surface.md
• docs/enterprise_proof/index.md
• docs/enterprise_proof/offtarget_public.md
• docs/enterprise_proof/roi.md
• docs/enterprise_proof/support_policy.md
• docs/enterprise_proof/teams_deploy_guide.md
• docs/evs_visual_tests.md
• docs/evs_visual.md
• docs/faq_v0_1.md
• docs/features_catalog.md
• docs/genome_editing_evidence_runtime_v0_1.md
• docs/getting-started.md
• docs/governance_contract.md
• docs/governed_predictor_adapters.md
• docs/helix_experiment_roadmap.md
• docs/helix_principles.md
• docs/helixspec_mvp.md
• docs/helixspec_quickstart.md
• docs/hub/end_to_end_v0.md
• docs/hub/example_bundle.md
• docs/hub/index.md
• docs/hub/investor_memo.md
• docs/hub/pilot.md
• docs/hub/pitch.md
• docs/hub/proof_url_v0.md
• docs/hub/review_v0.md
• docs/hub/rfcs/index.md
• docs/hub/rfcs/rfc_0001_bundle_spec_v1.md
• docs/hub/rfcs/rfc_0002_canonical_json_v1.md
• docs/hub/rfcs/rfc_0003_run_receipt_v1.md
• docs/hub/rfcs/rfc_0004_approval_surface_v1.md
• docs/hub/rfcs/rfc_0005_approval_receipt_v1.md
• docs/hub/rfcs/rfc_0006_audit_export_v1.md
• docs/hub/rfcs/rfc_0007_job_v1.md
• docs/hub/rfcs/rfc_0008_backend_fingerprint_v1.md
• docs/hub/rfcs/rfc_0009_decision_v1.md
• docs/hub/trust_model.md
• docs/index.md
• docs/instructions.md
• docs/lightcone_v0_9_milestone.md
• docs/model_limitations/crispr_edit_dag_limitations.md
• docs/never_do.md
• docs/non_goals.md
• docs/notebooks/edit_dag_visual_demo.ipynb
• docs/ogn_integration.md
• docs/omnis_helix_screenshots.md
• docs/omnis_helix_strategy.md
• docs/omnis_helix_tour.md
• docs/paper_deterministic_genome_editing.md
• docs/partner_intake.md
• docs/partner_ops_playbook.md
• docs/playground/index.html
• docs/playground/js/realtime_branch_chart.js
• docs/playground/js/realtime_compare.js
• docs/playground/js/realtime_worker.js
• docs/playground/js/realtime.js
• docs/playground/realtime.html
• docs/policies/compatibility_deprecation.md
• docs/policies/conformance.md
• docs/policies/export_governance.md
• docs/policies/external_attestation.md
• docs/policies/governance_registry_policy.md
• docs/policies/incident_playbook.md
• docs/policies/lean_bridge.md
• docs/policies/longevity.md
• docs/policies/observability.md
• docs/policies/off_target_constraint.md
• docs/policies/performance_contracts.md
• docs/policies/plugin_governance.md
• docs/policies/policy_controls.md
• docs/policies/release_provenance.md
• docs/policies/schema_hygiene.md
• docs/policies/security.md
• docs/policies/semantic_drift.md
• docs/policies/ux_onboarding.md
• docs/positioning.md
• docs/prime_physics.md
• docs/product_manual.md
• docs/proof_bundles.md
• docs/proofs/lightcone_demo_proof_v0_8.md
• docs/public_release_channel.md
• docs/pypi_publishing.md
• docs/rail_control_plane.md
• docs/reference_validation_bundle.md
• docs/reference/api.md
• docs/release_checklist.md
• docs/RELEASE_VERIFY.md
• docs/repo_audit_1b_thesis.json
• docs/repo_audit_1b_thesis.md
• docs/run_graph.md
• docs/run_ingest.md
• docs/runbooks/knockout_decision_gate_demo.md
• docs/runbooks/lightcone_runbook.md
• docs/schema-reference.md
• docs/schema.md
• docs/scientific_contract_v1.md
• docs/scoring_version.md
• docs/snapshot_spec_v1.md
• docs/snapshot_spec_v1.schema.json
• docs/studio/core_features.md
• docs/studio/plugins.md
• docs/switching_proof_excerpt.txt
• docs/switching_proof.md
• docs/teams_v0.md
• docs/threat_model.md
• docs/trust_kit.md
• docs/v0_5_milestone.md
• docs/validation_crispr_efficiency_panel.md
• docs/validation_crispr_offtarget_panel.md
• docs/validation_crispr_plasmid.md
• docs/validation_prime_panel.md
• docs/validation/README.md
• docs/veribiota.md
• docs/visualization/alignment-ribbon.md
• docs/visualization/distance-heatmap.md
• docs/visualization/minimizer-density.md
• docs/visualization/motif-logo.md
• docs/visualization/rna-dotplot.md
• docs/viz.md
• docs/wetlab_preflight_linter.md
• docs/whats-new.md
• docs/why_helix.md
• examples/delivery/README.md
• examples/offscreen_webrtc_demo/README_hw.md
• examples/offscreen_webrtc_demo/README.md
• examples/plugins/hello_world/README.md
• examples/plugins/remote_echo/README.md
• examples/plugins/remote_web_panel/README.md
• examples/proof/helix_editing_decisions_v1/README.md
• examples/README.md
• experiments/infrastructure_validation_suite/multi_site_reproducibility/README.md
• experiments/infrastructure_validation_suite/procurement_bundles/HELIX_IVS_PROCUREMENT_1.0.0_20260212_173410/README.md
• experiments/infrastructure_validation_suite/README.md
• experiments/README.md
• fixtures/golden_failing_bundle_v1/README.md
• fixtures/hostile_bypass_pack_v1/README.md
• outreach/README.md
• README.md
• repro/enzyme_contract_v1/README.md
• repro/helix_repro_bundle_v1/README.md
• repro/scientific_contract_v1/README.md
• schemas/evidence/README.md
• schemas/run/README.md
• schemas/species/README.md
• src/helix/campaigns/README.md
• src/helix/compute/README.md
• src/helix/datasets/evaluation_packs/helix_eval_v1_azimuth_public/README.md
• src/helix/datasets/evaluation_packs/helix_eval_v1_batch_demo/README.md
• src/helix/datasets/evaluation_packs/helix_eval_v1_offtarget_public_rloks_sensitive/README.md
• src/helix/datasets/evaluation_packs/helix_eval_v1_offtarget_public/README.md
• src/helix/datasets/validation_packs/ampseq_indel_profile_v1/README.md
• src/helix/datasets/validation_packs/bam_qc_coverage_v1/README.md
• src/helix/datasets/validation_packs/cas9_nhej_outcome_prediction_v1/README.md
• src/helix/datasets/validation_packs/crisprresso_import_v1/README.md
• src/helix/datasets/validation_packs/repro_bundle_v1/README.md
• src/helix/datasets/validation_packs/signed_plugin_trust_chain_v1/README.md
• src/helix/datasets/validation_packs/vcf_qc_annot_v1/README.md
• src/helix/studio/experimental/run_history_mv/README.md
• tests/fixtures/lightcone/README.md
• tests/systems/fixtures/benchmark_panel/README.md
• tests/veribiota/README.md
• tools/hubverifier-go/README.md
• Visualization_Bench/README.md

</details> <details> <summary>Citations:</summary>

• benchmarks/README.md
• deliver_workbench/README.md
• deploy/helm/helix-teams/README.md
• deploy/k8s/README.md
• deploy/README.md
• deploy/vastai/README.md
• design_partner/README.md
• design_partner/sessions/README.md
• docs/adr/0001-gui-monolith-refactor.md
• docs/artifacts.md
• docs/assets/viz/alignment-ribbon.json
• docs/assets/viz/alignment-ribbon.viz.json
• docs/assets/viz/crispr_playground_dag.json
• docs/assets/viz/distance-heatmap.json
• docs/assets/viz/distance-heatmap.viz.json
• docs/assets/viz/minimizers.json
• docs/assets/viz/minimizers.viz.json
• docs/assets/viz/motif-logo.json
• docs/assets/viz/motif-logo.viz.json
• docs/assets/viz/pcr_amplicon_dag.json
• docs/assets/viz/prime_playground_dag.json
• docs/assets/viz/rna-dotplot.json
• docs/assets/viz/rna-dotplot.viz.json
• docs/assets/viz/seed-chain.json
• docs/assets/viz/seed-chain.viz.json
• docs/audit_walkthrough.md
• docs/battlecards/benchling.md
• docs/benchmarks.md
• docs/billion_dollar_thesis.md
• docs/ci/verify_gate_template.md
• docs/ci/verify_reason_codes.md
• docs/cli_config_schema.md
• docs/cli_headless.md
• docs/cli.md
• docs/cli/alpha.md
• docs/cli/demo.md
• docs/cli/live.md
• docs/cli/pcr.md
• docs/cli/schema.md
• docs/cli/session_contract_v1.md
• docs/cli/session_contract_v2.md
• docs/cli/session_contract_v3.md
• docs/cli/viz.md
• docs/cli/workflows.md
• docs/competitive_landscape.md
• docs/concepts/artifacts.md
• docs/concepts/multiscale.md
• docs/concepts/outcome_digital_twin.md
• docs/concepts/perfection.md
• docs/concepts/schemas.md
• docs/concepts/workflows.md
• docs/contracts/enzyme_program_contract_v1.md
• docs/contracts/helix_1_0.md
• docs/contracts/lightcone_visual_contract_v0_8.md
• docs/contributing.md
• docs/crispr_ctmc_tau_leap.md
• docs/CROSS_HOST_PROTOCOL.md
• docs/decision_cockpit_demo.md
• docs/decision_support/spec_v0.md
• docs/design_partner_email_template.md
• docs/design_partner_program.md
• docs/dev_gpu_profiling.md
• docs/dev/ci_policy.md
• docs/dev/evs.md
• docs/dev/offtarget_heat.md
• docs/dev/packaging_pyinstaller.md
• docs/dev/renderer_fields.md
• docs/dev/SECURITY_HARDENING.md
• docs/dev/SECURITY_SCANNING.md
• docs/dev/ui.md
• docs/download.md
• docs/edit_dag_frames.md
• docs/edit_dag_overview.md
• docs/edit-dag-viz.md
• docs/engine_architecture.md
• docs/engine_cuda_plan.md
• docs/enterprise_proof/auroc_delta_demo.md
• docs/enterprise_proof/azimuth_public.md
• docs/enterprise_proof/evaluation_guide.md
• docs/enterprise_proof/government-ready-product-surface.md
• docs/enterprise_proof/index.md
• docs/enterprise_proof/offtarget_public.md
• docs/enterprise_proof/roi.md
• docs/enterprise_proof/support_policy.md
• docs/enterprise_proof/teams_deploy_guide.md
• docs/evs_visual_tests.md
• docs/evs_visual.md
• docs/faq_v0_1.md
• docs/features_catalog.md
• docs/genome_editing_evidence_runtime_v0_1.md
• docs/getting-started.md
• docs/governance_contract.md
• docs/governed_predictor_adapters.md
• docs/helix_experiment_roadmap.md
• docs/helix_principles.md
• docs/helixspec_mvp.md
• docs/helixspec_quickstart.md
• docs/hub/end_to_end_v0.md
• docs/hub/example_bundle.md
• docs/hub/index.md
• docs/hub/investor_memo.md
• docs/hub/pilot.md
• docs/hub/pitch.md
• docs/hub/proof_url_v0.md
• docs/hub/review_v0.md
• docs/hub/rfcs/index.md
• docs/hub/rfcs/rfc_0001_bundle_spec_v1.md
• docs/hub/rfcs/rfc_0002_canonical_json_v1.md
• docs/hub/rfcs/rfc_0003_run_receipt_v1.md
• docs/hub/rfcs/rfc_0004_approval_surface_v1.md
• docs/hub/rfcs/rfc_0005_approval_receipt_v1.md
• docs/hub/rfcs/rfc_0006_audit_export_v1.md
• docs/hub/rfcs/rfc_0007_job_v1.md
• docs/hub/rfcs/rfc_0008_backend_fingerprint_v1.md
• docs/hub/rfcs/rfc_0009_decision_v1.md
• docs/hub/trust_model.md
• docs/index.md
• docs/instructions.md
• docs/lightcone_v0_9_milestone.md
• docs/model_limitations/crispr_edit_dag_limitations.md
• docs/never_do.md
• docs/non_goals.md
• docs/notebooks/edit_dag_visual_demo.ipynb
• docs/ogn_integration.md
• docs/omnis_helix_screenshots.md
• docs/omnis_helix_strategy.md
• docs/omnis_helix_tour.md
• docs/paper_deterministic_genome_editing.md
• docs/partner_intake.md
• docs/partner_ops_playbook.md
• docs/playground/index.html
• docs/playground/js/realtime_branch_chart.js:1
• docs/playground/js/realtime_compare.js:42
• docs/playground/js/realtime_worker.js:100
• docs/playground/js/realtime.js:607
• docs/playground/realtime.html
• docs/policies/compatibility_deprecation.md
• docs/policies/conformance.md
• docs/policies/export_governance.md
• docs/policies/external_attestation.md
• docs/policies/governance_registry_policy.md
• docs/policies/incident_playbook.md
• docs/policies/lean_bridge.md
• docs/policies/longevity.md
• docs/policies/observability.md
• docs/policies/off_target_constraint.md
• docs/policies/performance_contracts.md
• docs/policies/plugin_governance.md
• docs/policies/policy_controls.md
• docs/policies/release_provenance.md
• docs/policies/schema_hygiene.md
• docs/policies/security.md
• docs/policies/semantic_drift.md
• docs/policies/ux_onboarding.md
• docs/positioning.md
• docs/prime_physics.md
• docs/product_manual.md
• docs/proof_bundles.md
• docs/proofs/lightcone_demo_proof_v0_8.md
• docs/public_release_channel.md
• docs/pypi_publishing.md
• docs/rail_control_plane.md
• docs/reference_validation_bundle.md
• docs/reference/api.md
• docs/release_checklist.md
• docs/RELEASE_VERIFY.md
• docs/repo_audit_1b_thesis.json
• docs/repo_audit_1b_thesis.md
• docs/run_graph.md
• docs/run_ingest.md
• docs/runbooks/knockout_decision_gate_demo.md
• docs/runbooks/lightcone_runbook.md
• docs/schema-reference.md
• docs/schema.md
• docs/scientific_contract_v1.md
• docs/scoring_version.md
• docs/snapshot_spec_v1.md
• docs/snapshot_spec_v1.schema.json
• docs/studio/core_features.md
• docs/studio/plugins.md
• docs/switching_proof_excerpt.txt
• docs/switching_proof.md
• docs/teams_v0.md
• docs/threat_model.md
• docs/trust_kit.md
• docs/v0_5_milestone.md
• docs/validation_crispr_efficiency_panel.md
• docs/validation_crispr_offtarget_panel.md
• docs/validation_crispr_plasmid.md
• docs/validation_prime_panel.md
• docs/validation/README.md
• docs/veribiota.md
• docs/visualization/alignment-ribbon.md
• docs/visualization/distance-heatmap.md
• docs/visualization/minimizer-density.md
• docs/visualization/motif-logo.md
• docs/visualization/rna-dotplot.md
• docs/viz.md
• docs/wetlab_preflight_linter.md
• docs/whats-new.md
• docs/why_helix.md
• examples/delivery/README.md
• examples/offscreen_webrtc_demo/README_hw.md
• examples/offscreen_webrtc_demo/README.md
• examples/plugins/hello_world/README.md
• examples/plugins/remote_echo/README.md
• examples/plugins/remote_web_panel/README.md
• examples/proof/helix_editing_decisions_v1/README.md
• examples/README.md
• experiments/infrastructure_validation_suite/multi_site_reproducibility/README.md
• experiments/infrastructure_validation_suite/procurement_bundles/HELIX_IVS_PROCUREMENT_1.0.0_20260212_173410/README.md
• experiments/infrastructure_validation_suite/README.md
• experiments/README.md
• fixtures/golden_failing_bundle_v1/README.md
• fixtures/hostile_bypass_pack_v1/README.md
• outreach/README.md
• README.md
• repro/enzyme_contract_v1/README.md
• repro/helix_repro_bundle_v1/README.md
• repro/scientific_contract_v1/README.md
• schemas/evidence/README.md
• schemas/run/README.md
• schemas/species/README.md
• src/helix/campaigns/README.md
• src/helix/compute/README.md
• src/helix/datasets/evaluation_packs/helix_eval_v1_azimuth_public/README.md
• src/helix/datasets/evaluation_packs/helix_eval_v1_batch_demo/README.md
• src/helix/datasets/evaluation_packs/helix_eval_v1_offtarget_public_rloks_sensitive/README.md
• src/helix/datasets/evaluation_packs/helix_eval_v1_offtarget_public/README.md
• src/helix/datasets/validation_packs/ampseq_indel_profile_v1/README.md
• src/helix/datasets/validation_packs/bam_qc_coverage_v1/README.md
• src/helix/datasets/validation_packs/cas9_nhej_outcome_prediction_v1/README.md
• src/helix/datasets/validation_packs/crisprresso_import_v1/README.md
• src/helix/datasets/validation_packs/repro_bundle_v1/README.md
• src/helix/datasets/validation_packs/signed_plugin_trust_chain_v1/README.md
• src/helix/datasets/validation_packs/vcf_qc_annot_v1/README.md
• src/helix/studio/experimental/run_history_mv/README.md
• tests/fixtures/lightcone/README.md
• tests/systems/fixtures/benchmark_panel/README.md
• tests/veribiota/README.md
• tools/hubverifier-go/README.md
• Visualization_Bench/README.md

</details>

Important Components

• Helix (application) at .: Helix python component
• helix-governance (application) at .: helix-governance python component
• src (module) at src: Source module rooted at src.
• Tests (tests) at tests: Repository tests and fixtures.
• Documentation (docs) at .: Repository documentation and wiki source files.
• engine/src (module) at engine/src: Source module rooted at engine/src.
• github.com/omniscoder/Helix/tools/hubverifier-go (application) at tools/hubverifier-go: github.com/omniscoder/Helix/tools/hubverifier-go go component
• src/helix_engine/src (module) at src/helix_engine/src: Source module rooted at src/helix_engine/src.
• offscreen-webrtc-signaling (application) at examples/offscreen_webrtc_demo/signaling: offscreen-webrtc-signaling node component
• helix (application) at .: Python script entrypoint helix.
• helix-campaign (application) at .: Python script entrypoint helix-campaign.
• helix-cli (application) at .: Python script entrypoint helix-cli.

<details> <summary>Related files:</summary>

• requirements-dev.txt
• src/helix_api.py
• src/helix_cuda_fields.py
• src/helix_engine/__init__.py
• pyproject.toml
• src/helix_engine/CMakeLists.txt
• deliver_workbench/tests/__init__.py
• deliver_workbench/tests/test_adapter_e2e.py
• deliver_workbench/tests/test_database.py
• deliver_workbench/tests/test_matchmaker.py
• benchmarks/README.md
• deliver_workbench/README.md
• deploy/helm/helix-teams/README.md
• deploy/k8s/README.md
• engine/src/helix/cuda/fields/composite_editability.cu
• engine/src/helix/cuda/fields/dcas9_occupancy.cu
• engine/src/helix/cuda/fields/gc_homopolymer.cu
• engine/src/helix/cuda/fields/indel_risk.cu
• tools/hubverifier-go/cmd/hubverify/main.go
• tools/hubverifier-go/go.mod
• tools/hubverifier-go/internal/c14n/c14n_test.go
• tools/hubverifier-go/internal/c14n/c14n.go
• src/helix_engine/src/binding.cpp
• src/helix_engine/src/ctmc_tau_leap_cuda.cu
• src/helix_engine/src/l0_thermo.cu
• src/helix_engine/src/physics_cuda.cu
• examples/offscreen_webrtc_demo/signaling/package.json
• examples/offscreen_webrtc_demo/signaling/server.js

</details> <details> <summary>Citations:</summary>

• requirements-dev.txt
• src/helix_api.py
• pyproject.toml
• src/helix_cuda_fields.py
• deliver_workbench/tests/__init__.py
• deliver_workbench/tests/test_adapter_e2e.py:16
• benchmarks/README.md
• deliver_workbench/README.md
• engine/src/helix/cuda/fields/composite_editability.cu
• engine/src/helix/cuda/fields/dcas9_occupancy.cu
• tools/hubverifier-go/cmd/hubverify/main.go:22
• tools/hubverifier-go/go.mod
• src/helix_engine/src/binding.cpp
• src/helix_engine/src/ctmc_tau_leap_cuda.cu
• examples/offscreen_webrtc_demo/signaling/package.json
• examples/offscreen_webrtc_demo/signaling/server.js:6

</details>

Citations

<details> <summary>Citations:</summary>

• benchmarks/README.md
• deliver_workbench/README.md
• deploy/helm/helix-teams/README.md
• deploy/k8s/README.md
• deploy/README.md
• deploy/vastai/README.md
• examples/offscreen_webrtc_demo/signaling/package.json
• examples/offscreen_webrtc_demo/signaling/server.js:6
• tools/hubverifier-go/cmd/hubverify/main.go:22
• tools/hubverifier-go/go.mod
• engine/src/helix/cuda/fields/composite_editability.cu
• engine/src/helix/cuda/fields/dcas9_occupancy.cu
• src/helix_api.py
• src/helix_cuda_fields.py
• src/helix_engine/__init__.py
• deliver_workbench/tests/__init__.py
• deliver_workbench/tests/test_adapter_e2e.py:16
• deliver_workbench/tests/test_database.py:25
• pyproject.toml
• design_partner/README.md
• design_partner/sessions/README.md
• docs/adr/0001-gui-monolith-refactor.md
• docs/artifacts.md
• docs/assets/viz/alignment-ribbon.json
• docs/assets/viz/alignment-ribbon.viz.json
• docs/assets/viz/crispr_playground_dag.json
• docs/assets/viz/distance-heatmap.json
• docs/assets/viz/distance-heatmap.viz.json
• docs/assets/viz/minimizers.json
• docs/assets/viz/minimizers.viz.json
• docs/assets/viz/motif-logo.json
• docs/assets/viz/motif-logo.viz.json
• docs/assets/viz/pcr_amplicon_dag.json
• docs/assets/viz/prime_playground_dag.json
• docs/assets/viz/rna-dotplot.json
• docs/assets/viz/rna-dotplot.viz.json
• docs/assets/viz/seed-chain.json
• docs/assets/viz/seed-chain.viz.json
• docs/audit_walkthrough.md
• docs/battlecards/benchling.md
• docs/benchmarks.md
• docs/billion_dollar_thesis.md
• docs/ci/verify_gate_template.md
• docs/ci/verify_reason_codes.md
• docs/cli_config_schema.md
• docs/cli_headless.md
• docs/cli.md
• docs/cli/alpha.md
• docs/cli/demo.md
• docs/cli/live.md
• docs/cli/pcr.md
• docs/cli/schema.md
• docs/cli/session_contract_v1.md
• docs/cli/session_contract_v2.md
• docs/cli/session_contract_v3.md
• docs/cli/viz.md
• docs/cli/workflows.md
• docs/competitive_landscape.md
• docs/concepts/artifacts.md
• docs/concepts/multiscale.md
• docs/concepts/outcome_digital_twin.md
• docs/concepts/perfection.md
• docs/concepts/schemas.md
• docs/concepts/workflows.md
• docs/contracts/enzyme_program_contract_v1.md
• docs/contracts/helix_1_0.md
• docs/contracts/lightcone_visual_contract_v0_8.md
• docs/contributing.md
• docs/crispr_ctmc_tau_leap.md
• docs/CROSS_HOST_PROTOCOL.md
• docs/decision_cockpit_demo.md
• docs/decision_support/spec_v0.md
• docs/design_partner_email_template.md
• docs/design_partner_program.md
• docs/dev_gpu_profiling.md
• docs/dev/ci_policy.md
• docs/dev/evs.md
• docs/dev/offtarget_heat.md
• docs/dev/packaging_pyinstaller.md
• docs/dev/renderer_fields.md
• docs/dev/SECURITY_HARDENING.md
• docs/dev/SECURITY_SCANNING.md
• docs/dev/ui.md
• docs/download.md
• docs/edit_dag_frames.md
• docs/edit_dag_overview.md
• docs/edit-dag-viz.md
• docs/engine_architecture.md
• docs/engine_cuda_plan.md
• docs/enterprise_proof/auroc_delta_demo.md
• docs/enterprise_proof/azimuth_public.md
• docs/enterprise_proof/evaluation_guide.md
• docs/enterprise_proof/government-ready-product-surface.md
• docs/enterprise_proof/index.md
• docs/enterprise_proof/offtarget_public.md
• docs/enterprise_proof/roi.md
• docs/enterprise_proof/support_policy.md
• docs/enterprise_proof/teams_deploy_guide.md
• docs/evs_visual_tests.md
• docs/evs_visual.md
• docs/faq_v0_1.md
• docs/features_catalog.md
• docs/genome_editing_evidence_runtime_v0_1.md
• docs/getting-started.md
• docs/governance_contract.md
• docs/governed_predictor_adapters.md
• docs/helix_experiment_roadmap.md
• docs/helix_principles.md
• docs/helixspec_mvp.md
• docs/helixspec_quickstart.md
• docs/hub/end_to_end_v0.md
• docs/hub/example_bundle.md
• docs/hub/index.md
• docs/hub/investor_memo.md
• docs/hub/pilot.md
• docs/hub/pitch.md
• docs/hub/proof_url_v0.md
• docs/hub/review_v0.md
• docs/hub/rfcs/index.md
• docs/hub/rfcs/rfc_0001_bundle_spec_v1.md
• docs/hub/rfcs/rfc_0002_canonical_json_v1.md
• docs/hub/rfcs/rfc_0003_run_receipt_v1.md
• docs/hub/rfcs/rfc_0004_approval_surface_v1.md
• docs/hub/rfcs/rfc_0005_approval_receipt_v1.md
• docs/hub/rfcs/rfc_0006_audit_export_v1.md
• docs/hub/rfcs/rfc_0007_job_v1.md
• docs/hub/rfcs/rfc_0008_backend_fingerprint_v1.md
• docs/hub/rfcs/rfc_0009_decision_v1.md
• docs/hub/trust_model.md
• docs/index.md
• docs/instructions.md
• docs/lightcone_v0_9_milestone.md
• docs/model_limitations/crispr_edit_dag_limitations.md
• docs/never_do.md
• docs/non_goals.md
• docs/notebooks/edit_dag_visual_demo.ipynb
• docs/ogn_integration.md
• docs/omnis_helix_screenshots.md
• docs/omnis_helix_strategy.md
• docs/omnis_helix_tour.md
• docs/paper_deterministic_genome_editing.md
• docs/partner_intake.md
• docs/partner_ops_playbook.md
• docs/playground/index.html
• docs/playground/js/realtime_branch_chart.js:1
• docs/playground/js/realtime_compare.js:42
• docs/playground/js/realtime_worker.js:100
• docs/playground/js/realtime.js:607
• docs/playground/realtime.html
• docs/policies/compatibility_deprecation.md
• docs/policies/conformance.md
• docs/policies/export_governance.md
• docs/policies/external_attestation.md
• docs/policies/governance_registry_policy.md
• docs/policies/incident_playbook.md
• docs/policies/lean_bridge.md
• docs/policies/longevity.md
• docs/policies/observability.md
• docs/policies/off_target_constraint.md
• docs/policies/performance_contracts.md
• docs/policies/plugin_governance.md
• docs/policies/policy_controls.md
• docs/policies/release_provenance.md
• docs/policies/schema_hygiene.md
• docs/policies/security.md
• docs/policies/semantic_drift.md
• docs/policies/ux_onboarding.md
• docs/positioning.md
• docs/prime_physics.md
• docs/product_manual.md
• docs/proof_bundles.md
• docs/proofs/lightcone_demo_proof_v0_8.md
• docs/public_release_channel.md
• docs/pypi_publishing.md
• docs/rail_control_plane.md
• docs/reference_validation_bundle.md
• docs/reference/api.md
• docs/release_checklist.md
• docs/RELEASE_VERIFY.md
• docs/repo_audit_1b_thesis.json
• docs/repo_audit_1b_thesis.md
• docs/run_graph.md
• docs/run_ingest.md
• docs/runbooks/knockout_decision_gate_demo.md
• docs/runbooks/lightcone_runbook.md
• docs/schema-reference.md
• docs/schema.md
• docs/scientific_contract_v1.md
• docs/scoring_version.md
• docs/snapshot_spec_v1.md
• docs/snapshot_spec_v1.schema.json
• docs/studio/core_features.md
• docs/studio/plugins.md
• docs/switching_proof_excerpt.txt
• docs/switching_proof.md
• docs/teams_v0.md
• docs/threat_model.md
• docs/trust_kit.md
• docs/v0_5_milestone.md
• docs/validation_crispr_efficiency_panel.md
• docs/validation_crispr_offtarget_panel.md
• docs/validation_crispr_plasmid.md
• docs/validation_prime_panel.md
• docs/validation/README.md
• docs/veribiota.md
• docs/visualization/alignment-ribbon.md
• docs/visualization/distance-heatmap.md
• docs/visualization/minimizer-density.md
• docs/visualization/motif-logo.md
• docs/visualization/rna-dotplot.md
• docs/viz.md
• docs/wetlab_preflight_linter.md
• docs/whats-new.md
• docs/why_helix.md
• examples/delivery/README.md
• examples/offscreen_webrtc_demo/README_hw.md
• examples/offscreen_webrtc_demo/README.md
• examples/plugins/hello_world/README.md
• examples/plugins/remote_echo/README.md
• examples/plugins/remote_web_panel/README.md
• examples/proof/helix_editing_decisions_v1/README.md
• examples/README.md
• experiments/infrastructure_validation_suite/multi_site_reproducibility/README.md
• experiments/infrastructure_validation_suite/procurement_bundles/HELIX_IVS_PROCUREMENT_1.0.0_20260212_173410/README.md
• experiments/infrastructure_validation_suite/README.md
• experiments/README.md
• fixtures/golden_failing_bundle_v1/README.md
• fixtures/hostile_bypass_pack_v1/README.md
• outreach/README.md
• README.md
• repro/enzyme_contract_v1/README.md
• repro/helix_repro_bundle_v1/README.md
• repro/scientific_contract_v1/README.md
• schemas/evidence/README.md
• schemas/run/README.md
• schemas/species/README.md
• src/helix/campaigns/README.md
• src/helix/compute/README.md
• src/helix/datasets/evaluation_packs/helix_eval_v1_azimuth_public/README.md
• src/helix/datasets/evaluation_packs/helix_eval_v1_batch_demo/README.md
• src/helix/datasets/evaluation_packs/helix_eval_v1_offtarget_public_rloks_sensitive/README.md
• src/helix/datasets/evaluation_packs/helix_eval_v1_offtarget_public/README.md
• src/helix/datasets/validation_packs/ampseq_indel_profile_v1/README.md
• src/helix/datasets/validation_packs/bam_qc_coverage_v1/README.md
• src/helix/datasets/validation_packs/cas9_nhej_outcome_prediction_v1/README.md
• src/helix/datasets/validation_packs/crisprresso_import_v1/README.md
• src/helix/datasets/validation_packs/repro_bundle_v1/README.md
• src/helix/datasets/validation_packs/signed_plugin_trust_chain_v1/README.md
• src/helix/datasets/validation_packs/vcf_qc_annot_v1/README.md
• src/helix/studio/experimental/run_history_mv/README.md
• tests/fixtures/lightcone/README.md
• tests/systems/fixtures/benchmark_panel/README.md
• tests/veribiota/README.md
• tools/hubverifier-go/README.md
• Visualization_Bench/README.md
• requirements-dev.txt
• src/helix_engine/src/binding.cpp
• src/helix_engine/src/ctmc_tau_leap_cuda.cu

</details>