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    "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/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/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:tests/fixtures/lightcone/README.md",
    "ingest:file:tests/systems/fixtures/benchmark_panel/README.md",
    "ingest:file:tests/veribiota/README.md",
    "ingest:file:tools/hubverifier-go/README.md",
    "ingest:file:Visualization_Bench/README.md"
  ],
  "qualityWarnings": []
}
</details>

Documentation

Repository documentation and wiki source files.

Implementation Roles

Insufficient evidence to infer implementation roles confidently.

<details> <summary>Supporting citations:</summary>
  • none
</details>

Module Responsibilities

Insufficient evidence to infer module responsibilities confidently.

<details> <summary>Supporting citations:</summary>
  • none
</details>

Key Symbols

applyFrame (function)

Behavior: Implements component logic in docs/playground/js/realtime.js by coordinating nearby symbol calls. It directly calls applyOutcomeFilters, changeSummary. Receives: Called by loadFrameAt, playFrames. Produces or triggers: Triggers applyOutcomeFilters, changeSummary, displayLines. Connected symbols:

  • Callers: loadFrameAt, playFrames.
  • Callees: applyOutcomeFilters, changeSummary, displayLines. Supporting implementation citations:
  • docs/playground/js/realtime.js:155
  • docs/playground/js/realtime.js:393
  • docs/playground/js/realtime.js:688

computeFrames (function)

Behavior: Implements component logic in docs/playground/js/realtime_worker.js by coordinating nearby symbol calls. It directly calls map, mismatchCount. Receives: Called by frames. Produces or triggers: Triggers map, mismatchCount, pamMatches. Connected symbols:

  • Callers: frames.
  • Callees: map, mismatchCount, pamMatches. Supporting implementation citations:
  • docs/playground/js/realtime_worker.js:62
  • docs/playground/js/realtime_worker.js:381
  • docs/playground/js/realtime_worker.js:54

displayLines (function)

Behavior: Implements component logic in docs/playground/js/realtime.js by coordinating nearby symbol calls. It directly calls changeSummary, mechanismFromRule. Receives: Called by applyFrame, lines, lines. Produces or triggers: Triggers changeSummary, mechanismFromRule, String. Connected symbols:

  • Callers: applyFrame, lines, lines.
  • Callees: changeSummary, mechanismFromRule, String. Supporting implementation citations:
  • docs/playground/js/realtime.js:214
  • docs/playground/js/realtime.js:155
  • docs/playground/js/realtime.js:169
<details> <summary>Related files:</summary>
  • docs/playground/js/realtime.js
  • docs/playground/js/realtime_worker.js
</details> <details> <summary>Citations:</summary>
  • docs/playground/js/realtime.js:155
  • docs/playground/js/realtime.js:393
  • docs/playground/js/realtime.js:688
  • docs/playground/js/realtime_worker.js:62
  • docs/playground/js/realtime_worker.js:381
  • docs/playground/js/realtime_worker.js:54
  • docs/playground/js/realtime.js:214
  • docs/playground/js/realtime.js:169
</details>

State Boundaries

Validated at:

  • Likely validated at parseExons in docs/playground/js/realtime_worker.js; this is inferred from validation-like naming rather than proved full program semantics. Validate with Run make (build) from .. Run helix-pilot-verify (run) from .. Run python -m pytest (test) from ..

Mutated in:

  • Likely mutated in updateBranchChart in docs/playground/js/realtime_branch_chart.js; this marks an inferred state-change boundary, not a formal dataflow proof. Nearby interface context: docs/snapshot_spec_v1.schema.json (schema) via docs/snapshot_spec_v1.schema.json.

Persisted or emitted through:

  • none
<details> <summary>Supporting citations:</summary>
  • docs/playground/js/realtime_worker.js:93
  • docs/playground/js/realtime_branch_chart.js:34
  • docs/snapshot_spec_v1.schema.json
  • Makefile
  • pyproject.toml
</details> <details> <summary>Related files:</summary>
  • docs/playground/js/realtime_worker.js
  • docs/playground/js/realtime.js
  • docs/playground/js/realtime_branch_chart.js
  • docs/playground/js/realtime_compare.js
  • docs/snapshot_spec_v1.schema.json
  • Makefile
  • pyproject.toml
</details> <details> <summary>Citations:</summary>
  • docs/playground/js/realtime_worker.js:93
  • docs/playground/js/realtime_branch_chart.js:34
  • docs/snapshot_spec_v1.schema.json
  • Makefile
  • pyproject.toml
</details>

State Ownership and Handoffs

Insufficient evidence to infer state ownership and handoffs confidently.

<details> <summary>Supporting citations:</summary>
  • none
</details>

Request Lifecycle

Insufficient evidence to infer a bounded request lifecycle confidently.

<details> <summary>Supporting citations:</summary>
  • none
</details>

Responsibilities

Repository documentation and wiki source files.

Type: docs Root path: . Ecosystem: unknown

<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
</details> <details> <summary>Citations:</summary>
  • benchmarks/README.md
  • deliver_workbench/README.md
  • deploy/helm/helix-teams/README.md
  • deploy/k8s/README.md
</details>

Entrypoints and Runtime Surface

  • none

Interfaces and Config

  • docs/snapshot_spec_v1.schema.json (schema) from docs/snapshot_spec_v1.schema.json
<details> <summary>Related files:</summary>
  • docs/snapshot_spec_v1.schema.json
</details> <details> <summary>Citations:</summary>
  • docs/snapshot_spec_v1.schema.json
</details>

Dependencies and Relationships

  • none
<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
</details> <details> <summary>Citations:</summary>
  • benchmarks/README.md
  • deliver_workbench/README.md
  • deploy/helm/helix-teams/README.md
  • deploy/k8s/README.md
</details>

Why This Hotspot Matters

Architectural role: Hotspot score 1713 with 491 inbound and 78 outbound inferred edges marks Documentation as a coordination-heavy component. It bridges src, tools.

Main coupling surfaces:

  • Owned interfaces: docs/snapshot_spec_v1.schema.json.
  • Call-heavy surface with 569 inferred call edges.

Likely failure modes:

  • Upstream breakage risk: 491 inbound edges suggest downstream callers depend on this boundary staying stable.
  • Coordination risk: 78 outbound edges mean changes can ripple into neighboring components.
  • Cross-subsystem regression risk: changes can disrupt handoffs across src, tools.
<details> <summary>Supporting citations:</summary>
  • benchmarks/README.md
  • deliver_workbench/README.md
  • deploy/helm/helix-teams/README.md
  • deploy/k8s/README.md
  • docs/snapshot_spec_v1.schema.json
</details> <details> <summary>Related files:</summary>
  • benchmarks/README.md
  • deliver_workbench/README.md
  • deploy/helm/helix-teams/README.md
  • deploy/k8s/README.md
  • docs/snapshot_spec_v1.schema.json
</details> <details> <summary>Citations:</summary>
  • benchmarks/README.md
  • deliver_workbench/README.md
  • deploy/helm/helix-teams/README.md
  • deploy/k8s/README.md
  • docs/snapshot_spec_v1.schema.json
</details>

Operational Risk Surface

Likely fault domains:

  • Risk-sensitive configuration paths: deploy/docker-compose.yml.
  • Cross-subsystem handoffs: src, tools.

High-cost dependencies:

  • 491 inbound edges raise the cost of breaking this component's callers.

First validation checks:

  • Run make (build) from ..
  • Run helix-pilot-verify (run) from ..
  • Run python -m pytest (test) from ..
  • Recheck behavior controlled by deploy/docker-compose.yml after the change.
<details> <summary>Supporting citations:</summary>
  • benchmarks/README.md
  • deliver_workbench/README.md
  • deploy/helm/helix-teams/README.md
  • deploy/docker-compose.yml
  • Makefile
  • pyproject.toml
</details> <details> <summary>Related files:</summary>
  • benchmarks/README.md
  • deliver_workbench/README.md
  • deploy/helm/helix-teams/README.md
  • deploy/docker-compose.yml
  • Makefile
  • pyproject.toml
</details> <details> <summary>Citations:</summary>
  • benchmarks/README.md
  • deliver_workbench/README.md
  • deploy/helm/helix-teams/README.md
  • deploy/docker-compose.yml
  • Makefile
  • pyproject.toml
</details>

Invariants and Failure Handling

Insufficient evidence to infer invariants and failure handling confidently.

<details> <summary>Supporting citations:</summary>
  • none
</details>

Where to Edit

Likely change entry files:

  • docs/snapshot_spec_v1.schema.json
  • benchmarks/README.md
  • deliver_workbench/README.md
  • deploy/helm/helix-teams/README.md

Owned interfaces:

  • docs/snapshot_spec_v1.schema.json (schema) from docs/snapshot_spec_v1.schema.json

Nearby verification surfaces:

  • Run make (build) from ..
  • Run helix (run) from ..
  • Run helix-campaign (run) from ..
  • Run helix-cli (run) from ..
<details> <summary>Supporting citations:</summary>
  • docs/snapshot_spec_v1.schema.json
  • benchmarks/README.md
  • deliver_workbench/README.md
  • deploy/helm/helix-teams/README.md
  • Makefile
  • pyproject.toml
</details> <details> <summary>Related files:</summary>
  • docs/snapshot_spec_v1.schema.json
  • benchmarks/README.md
  • deliver_workbench/README.md
  • deploy/helm/helix-teams/README.md
  • Makefile
  • pyproject.toml
</details> <details> <summary>Citations:</summary>
  • docs/snapshot_spec_v1.schema.json
  • benchmarks/README.md
  • deliver_workbench/README.md
  • deploy/helm/helix-teams/README.md
  • Makefile
  • pyproject.toml
</details>

Change Planning

Impacted areas:

  • Cross-subsystem risk touches src, tools.
  • Hotspot score 1713 with 491 inbound and 78 outbound edges suggests higher coordination risk.

Suggested verification steps:

  • Run make (build) from ..
  • Run helix (run) from ..
  • Run helix-campaign (run) from ..
  • Run helix-cli (run) from ..
<details> <summary>Supporting citations:</summary>
  • benchmarks/README.md
  • deliver_workbench/README.md
  • deploy/helm/helix-teams/README.md
  • Makefile
  • pyproject.toml
</details> <details> <summary>Related files:</summary>
  • benchmarks/README.md
  • deliver_workbench/README.md
  • deploy/helm/helix-teams/README.md
  • deploy/k8s/README.md
  • Makefile
  • pyproject.toml
</details> <details> <summary>Citations:</summary>
  • benchmarks/README.md
  • deliver_workbench/README.md
  • deploy/helm/helix-teams/README.md
  • Makefile
  • pyproject.toml
</details>

Nearby Workflows

  • make (build)
  • helix (run)
  • helix-campaign (run)
  • helix-cli (run)
  • helix-pilot-verify (run)
  • helix-studio (run)
  • omnis-helix (run)
  • python -m pytest (test)
<details> <summary>Related files:</summary>
  • Makefile
  • pyproject.toml
</details> <details> <summary>Citations:</summary>
  • Makefile
  • pyproject.toml
</details>

Citations

<details> <summary>Citations:</summary>
  • docs/playground/js/realtime.js:155
  • docs/playground/js/realtime.js:393
  • docs/playground/js/realtime.js:688
  • docs/playground/js/realtime_worker.js:62
  • docs/playground/js/realtime_worker.js:381
  • docs/playground/js/realtime_worker.js:54
  • docs/playground/js/realtime.js:214
  • docs/playground/js/realtime.js:169
  • docs/playground/js/realtime_worker.js:93
  • docs/playground/js/realtime_branch_chart.js:34
  • docs/snapshot_spec_v1.schema.json
  • Makefile
  • pyproject.toml
  • benchmarks/README.md
  • deliver_workbench/README.md
  • deploy/helm/helix-teams/README.md
  • deploy/k8s/README.md
  • deploy/docker-compose.yml
</details>