BioactivityDataAcquisition/mkdocs.yml at main · SatoryKono/BioactivityDataAcquisition · GitHub

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# mkdocs.yml
site_name: BioETL Project
site_url: https://SatoryKono.github.io/BioactivityDataAcquisition/
repo_url: https://github.com/SatoryKono/BioactivityDataAcquisition
repo_name: SatoryKono/BioactivityDataAcquisition
edit_uri: "edit/main/docs/"
site_dir: site
exclude_docs: |
    D-*.md
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not_in_nav: |
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    00-project/ai/skills/_references/**
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    00-project/ai/skills/local/prometheus-query-debugger/SKILL.md
    00-project/ai/skills/local/prometheus-rule-testing/SKILL.md
    04-reference/templates/adr-template.md
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    04-reference/templates/control-plane-contract-spec-template.md
    04-reference/templates/data-contract-spec-template.md
    04-reference/templates/pipeline-spec-template.md
    04-reference/templates/provider-spec-template.md
    04-reference/templates/runbook-template.md
    05-operations/deployment/mcp-neo4j-memory-final-summary.md
# Rendered SVG/PNG diagram images may be generated locally or in CI
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validation:
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theme:
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extra_javascript:
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# Responsive diagram styles
extra_css:
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# Navigation structure
nav:
    -   Home: 00-project/index.md
    -   "Project Map": 00-project/00-map.md
    -   "Project Rules":
            -   "RULES": 00-project/RULES.md
            -   "Requirements": 01-requirements/REQUIREMENTS.md
            -   "Rules Summary": 00-project/rules-summary.md
            -   "Glossary": 00-project/glossary.md
            -   "Tools Hub": 00-project/TOOLS.md
            -   Governance:
                    -   "D-01 Documentation Governance": 00-project/governance/01-documentation-governance-style-guide.md
                    -   "Naming Policy": 00-project/governance/02-naming-policy.md
                    -   "File Policy": 00-project/governance/03-file-policy.md
                    -   "Extending BioETL": 00-project/governance/04-extending-bioetl.md
                    -   "GitHub Policy": 00-project/governance/05-github-policy.md
                    -   "Docs Publication Policy": 00-project/governance/06-doc-publication-policy.md
                    -   "Docs Navigation Policy": 00-project/governance/07-doc-nav-policy.md
                    -   "Debt Ownership Playbook": 00-project/governance/08-debt-ownership-playbook.md
    -   Architecture:
            -   "Overview": 02-architecture/00-overview.md
            -   Layers:
                    -   "Domain": 02-architecture/01-domain-layer.md
                    -   "Application": 02-architecture/02-application-layer.md
                    -   "Infrastructure": 02-architecture/03-infrastructure-layer.md
                    -   "Interfaces": 02-architecture/04-interfaces-layer.md
                    -   "Composition": 02-architecture/05-composition-layer.md
            -   "System Context": 02-architecture/system-context.md
            -   "Container Diagram": 02-architecture/diagrams/guide/container-reference.md
            -   "Data Flow": 02-architecture/diagrams/guide/data-flow-reference.md
            -   "Data Layers": 02-architecture/data-layers.md
            -   "Observability Layers": 02-architecture/observability-layers.md
            -   "Module Dependency Map": 02-architecture/generated/module-dependency-map.md
            -   Diagrams:
                    -   "Overview": 02-architecture/diagrams/guide/index.md
                    -   "Diagram Policy": 02-architecture/diagrams/governance/policy.md
                    -   "Historical Diagram Catalog": 02-architecture/diagrams/governance/diagram-catalog.md
                    -   "Diagram Index": 02-architecture/diagrams/governance/diagrams-index.md
                    -   "Views Inventory": 02-architecture/diagrams/governance/diagram-views-inventory.md
                    -   "Workflow Guide": 02-architecture/diagrams/governance/DIAGRAM-WORKFLOW-GUIDE.md
            -   Decisions:
                    -   "Index": 02-architecture/decisions/README.md
                    -   "ADR-001 Delta Lake vs Parquet": 02-architecture/decisions/ADR-001-delta-lake-vs-parquet.md
                    -   "ADR-002 Medallion Architecture": 02-architecture/decisions/ADR-002-medallion-architecture.md
                    -   "ADR-003 In-Memory Locking": 02-architecture/decisions/ADR-003-in-memory-locking-strategy.md
                    -   "ADR-004 Pydantic vs Dataclasses": 02-architecture/decisions/ADR-004-pydantic-vs-dataclasses.md
                    -   "ADR-005 Composition Layer": 02-architecture/decisions/ADR-005-composition-layer-separation.md
                    -   "ADR-006 Logger & Metrics Ports": 02-architecture/decisions/ADR-006-logger-metrics-ports.md
                    -   "ADR-007 Circuit Breaker": 02-architecture/decisions/ADR-007-circuit-breaker-implementation.md
                    -   "ADR-008 Graceful Shutdown": 02-architecture/decisions/ADR-008-graceful-shutdown-strategy.md
                    -   "ADR-009 Paginated Fetcher": 02-architecture/decisions/ADR-009-paginated-fetcher-mixin.md
                    -   "ADR-010 Local-Only Deployment": 02-architecture/decisions/ADR-010-local-only-deployment.md
                    -   "ADR-011 Remove Watermark": 02-architecture/decisions/ADR-011-remove-watermark-mechanism.md
                    -   "ADR-012 Storage Clear Contract": 02-architecture/decisions/ADR-012-storage-clear-contract-and-run-id.md
                    -   "ADR-013 Async Storage Cleanup": 02-architecture/decisions/ADR-013-async-storage-cleanup.md
                    -   "ADR-014 Deterministic Writes": 02-architecture/decisions/ADR-014-deterministic-writes.md
                    -   "ADR-015 Pipeline Lifecycle": 02-architecture/decisions/ADR-015-pipeline-services-lifecycle.md
                    -   "ADR-016 Error Handling": 02-architecture/decisions/ADR-016-error-handling-strategy.md
                    -   "ADR-017 Observability Architecture": 02-architecture/decisions/ADR-017-observability-architecture.md
                    -   "ADR-018 Gold Strict Validation": 02-architecture/decisions/ADR-018-gold-strict-validation.md
                    -   "ADR-019 Observability Port Enforcement": 02-architecture/decisions/ADR-019-observability-port-enforcement.md
                    -   "ADR-020 BasePipeline Decomposition": 02-architecture/decisions/ADR-020-basepipeline-decomposition.md
                    -   "ADR-021 DDD Aggregates": 02-architecture/decisions/ADR-021-ddd-aggregates-adoption.md
                    -   "ADR-022 Tracing NoOp": 02-architecture/decisions/ADR-022-tracing-noop.md
                    -   "ADR-023 Entity Type Patterns": 02-architecture/decisions/ADR-023-entity-type-patterns.md
                    -   "ADR-024 Entity Naming Unification": 02-architecture/decisions/ADR-024-entity-naming-unification.md
                    -   "ADR-025 Pipeline Config Unification": 02-architecture/decisions/ADR-025-pipeline-config-unification.md
                    -   "ADR-026 Composite Pipeline Pattern": 02-architecture/decisions/ADR-026-composite-pipeline-pattern.md
                    -   "ADR-027 DQ Rules Externalization": 02-architecture/decisions/ADR-027-dq-rules-externalization.md
                    -   "ADR-028 Filter Rules Externalization": 02-architecture/decisions/ADR-028-filter-rules-externalization.md
                    -   "ADR-029 Output Metadata Unification": 02-architecture/decisions/ADR-029-output-metadata-unification.md
                    -   "ADR-030 Publication Pagination": 02-architecture/decisions/ADR-030-publication-pagination-strategy.md
                    -   "ADR-031 Loading Strategy": 02-architecture/decisions/ADR-031-loading-strategy-formalization.md
                    -   "ADR-032 Unified HTTP Client": 02-architecture/decisions/ADR-032-unified-http-client.md
                    -   "ADR-033 Publication Validation": 02-architecture/decisions/ADR-033-publication-validation-strategy.md
                    -   "ADR-034 Schema↔Domain Pairs": 02-architecture/decisions/ADR-034-schema-domain-pairs.md
                    -   "ADR-035 JSON Field Typing": 02-architecture/decisions/ADR-035-json-field-typing-policy.md
                    -   "ADR-036 Gold Contract Versioning": 02-architecture/decisions/ADR-036-gold-contract-versioning-policy.md
                    -   "ADR-037 Canonical Schema Generation": 02-architecture/decisions/ADR-037-canonical-schema-generation.md
                    -   "ADR-038 Enum Externalization": 02-architecture/decisions/ADR-038-enum-externalization.md
                    -   "ADR-039 Unified Entity Config": 02-architecture/decisions/ADR-039-unified-entity-config-format.md
                    -   "ADR-040 Diagram Governance": 02-architecture/decisions/ADR-040-diagram-governance.md
                    -   "ADR-041 Naming Policy Skills Agents": 02-architecture/decisions/ADR-041-naming-policy-skills-agents.md
                    -   "ADR-042 Testing Strategy Matrix": 02-architecture/decisions/ADR-042-testing-strategy-matrix.md
                    -   "ADR-043 Documentation Knowledge Management": 02-architecture/decisions/ADR-043-documentation-knowledge-management.md
                    -   "ADR-044 Run Manifest and Run Ledger": 02-architecture/decisions/ADR-044-run-manifest-ledger-control-plane.md
                    -   "ADR-045 Data Quality Contract System": 02-architecture/decisions/ADR-045-dq-contract-system.md
                    -   "Quality Gates Stabilization Notes": 02-architecture/decisions/notes/2026-03-04-quality-gates-stabilization.md
    -   Guides:
            -   "Overview": 03-guides/index.md
            -   "Getting Started": 03-guides/getting-started.md
            -   "Quick Start": 03-guides/quick-start.md
            -   "Docs Verification": 03-guides/docs-verification.md
            -   "Running Pipelines": 03-guides/running-pipelines.md
            -   "GitHub Local Workflow": 03-guides/github-local-workflow.md
            -   "Pipeline Configuration": 03-guides/pipeline-configuration.md
            -   "Pipeline Lifecycle": 03-guides/pipeline-lifecycle.md
            -   "DQ Configuration": 03-guides/dq-configuration.md
            -   "Publication Validation": 03-guides/publication-validation-guide.md
            -   "Date Handling": 03-guides/date-handling.md
            -   "Local Storage Layout": 03-guides/local-storage-layout.md
            -   "Metrics & Monitoring": 03-guides/metrics-monitoring.md
            -   "Testing": 03-guides/testing.md
            -   "Coverage Configuration": 03-guides/coverage-configuration.md
            -   "Test Optimization": 03-guides/test-optimization-guide.md
            -   "Troubleshooting": 03-guides/troubleshooting.md
            -   "Add New Source": 03-guides/add-new-source.md
            -   "Add Pipeline (Existing Source)": 03-guides/add-pipeline-existing-source.md
            -   "Cleanup Policy": 03-guides/cleanup-policy.md
            -   "Registry Pattern": 03-guides/registry-pattern.md
            -   "Config Schema Guidelines": 03-guides/development/config-schema-guidelines.md
            -   "Codex WSL2 Setup": 03-guides/development/codex-wsl2-setup.md
            -   Dashboards:
                    -   "Overview": 03-guides/dashboards/README.md
                    -   "V2 Updates": 03-guides/dashboards/dashboard-v2-updates.md
                    -   "V2 Usage": 03-guides/dashboards/dashboard-v2-usage.md
                    -   "Extension Guides":
                            -   "Human": 03-guides/dashboards/dashboard-extension-human.md
                            -   "LLM": 03-guides/dashboards/dashboard-extension-llm.md
                    -   "Monitoring Index": 03-guides/dashboards/monitoring-index.md
                    -   "Variables Guide": 03-guides/dashboards/variables-guide.md
            -   "File Path Audit Report": 03-guides/file-path-audit-report.md
    -   Engineering:
            -   "Overview": 05-engineering/README.md
            -   "Normalization Plan P0-P6": 05-engineering/normalization-plan-P0-P6.md
    -   Providers:
            -   "Overview": 04-reference/providers/README.md
            -   ChEMBL:
                    -   "Activity": 04-reference/providers/chembl/activity.md
                    -   "Assay": 04-reference/providers/chembl/assay.md
                    -   "Assay Parameters": 04-reference/providers/chembl/assay-parameters.md
                    -   "Cell Line": 04-reference/providers/chembl/cell-line.md
                    -   "Compound Record": 04-reference/providers/chembl/compound-record.md
                    -   "Molecule": 04-reference/providers/chembl/molecule.md
                    -   "Protein Class": 04-reference/providers/chembl/protein-class.md
                    -   "Publication": 04-reference/providers/chembl/publication.md
                    -   "Publication Similarity": 04-reference/providers/chembl/publication-similarity.md
                    -   "Publication Term": 04-reference/providers/chembl/publication-term.md
                    -   "Target": 04-reference/providers/chembl/target.md
                    -   "Target Component": 04-reference/providers/chembl/target-component.md
                    -   "Subcellular Fraction": 04-reference/providers/chembl/subcellular-fraction.md
                    -   "Tissue": 04-reference/providers/chembl/tissue.md
            -   PubChem:
                    -   "Compound": 04-reference/providers/pubchem/compound.md
            -   UniProt:
                    -   "Protein": 04-reference/providers/uniprot/protein.md
                    -   "ID Mapping": 04-reference/providers/uniprot/idmapping.md
            -   PubMed:
                    -   "Publication": 04-reference/providers/pubmed/publication.md
            -   CrossRef:
                    -   "Publication": 04-reference/providers/crossref/publication.md
            -   OpenAlex:
                    -   "Publication": 04-reference/providers/openalex/publication.md
            -   SemanticScholar:
                    -   "Publication": 04-reference/providers/semanticscholar/publication.md
    -   Pipelines:
            -   "Overview": 04-reference/pipelines/README.md
            -   "Publication Pipelines": 04-reference/pipelines/INDEX.md
            -   ChEMBL:
                    -   "Protein Class": 04-reference/pipelines/chembl/01-protein-class-spec.md
                    -   "Cell Line": 04-reference/pipelines/chembl/02-cell-line-spec.md
                    -   "Molecule": 04-reference/pipelines/chembl/03-molecule-spec.md
                    -   "Target": 04-reference/pipelines/chembl/04-target-spec.md
                    -   "Activity": 04-reference/pipelines/chembl/05-activity-spec.md
                    -   "Assay": 04-reference/pipelines/chembl/06-assay-spec.md
                    -   "Publication": 04-reference/pipelines/chembl/07-publication-spec.md
                    -   "Assay Parameters": 04-reference/pipelines/chembl/08-assay-parameters-spec.md
                    -   "Compound Record": 04-reference/pipelines/chembl/09-compound-record-spec.md
                    -   "Target Component": 04-reference/pipelines/chembl/10-target-component-spec.md
                    -   "Publication Term": 04-reference/pipelines/chembl/11-publication-term-spec.md
                    -   "Publication Similarity": 04-reference/pipelines/chembl/12-publication-similarity-spec.md
                    -   "Subcellular Fraction": 04-reference/pipelines/chembl/14-subcellular-fraction-spec.md
                    -   "Tissue": 04-reference/pipelines/chembl/15-tissue-spec.md
            -   PubChem:
                    -   "Compound": 04-reference/pipelines/pubchem/01-compound-spec.md
            -   UniProt:
                    -   "Protein": 04-reference/pipelines/uniprot/01-protein-spec.md
                    -   "ID Mapping": 04-reference/pipelines/uniprot/02-idmapping-spec.md
            -   PubMed:
                    -   "Publication": 04-reference/pipelines/pubmed/01-publication-spec.md
            -   CrossRef:
                    -   "Publication": 04-reference/pipelines/crossref/01-publication-spec.md
            -   OpenAlex:
                    -   "Publication": 04-reference/pipelines/openalex/01-publication-spec.md
            -   SemanticScholar:
                    -   "Publication": 04-reference/pipelines/semanticscholar/01-publication-spec.md
            -   Composite:
                    -   "Publication": 04-reference/pipelines/composite/01-publication-spec.md
                    -   "Molecule": 04-reference/pipelines/composite/02-molecule-spec.md
                    -   "Target": 04-reference/pipelines/composite/03-target-spec.md
                    -   "Activity": 04-reference/pipelines/composite/04-activity-spec.md
                    -   "Assay": 04-reference/pipelines/composite/05-assay-spec.md
    -   "Data Contracts":
            -   "Gold Schemas": 04-reference/contracts/gold-schemas.md
            -   "Data Quality Contracts": 04-reference/contracts/dq-contracts.md
            -   "Observability Metrics": 04-reference/contracts/observability.md
            -   "Run Manifest & Ledger": 04-reference/contracts/run-manifest-ledger.md
    -   Reference:
            -   "Reference Index": 04-reference/index.md
            -   CLI: 04-reference/cli.md
            -   Templates: 04-reference/templates/index.md
            -   API:
                    -   Overview: 04-reference/api/index.md
                    -   Domain:
                            -   "Domain API": 04-reference/api/domain.md
                            -   "Entities": 04-reference/api/domain/entities.md
                            -   "Ports": 04-reference/api/domain/ports.md
                            -   "Types": 04-reference/api/domain/types.md
                            -   "Exceptions": 04-reference/api/domain/exceptions.md
                    -   Application:
                            -   "Application API": 04-reference/api/application.md
                            -   "Core": 04-reference/api/application/core.md
                            -   "Pipelines": 04-reference/api/application/pipelines.md
                            -   "Services": 04-reference/api/application/services.md
                            -   "Transformers": 04-reference/api/application/transformers.md
                    -   Infrastructure:
                            -   "Infrastructure API": 04-reference/api/infrastructure.md
                            -   "Adapters": 04-reference/api/infrastructure/adapters.md
                            -   "Adapters Common": 04-reference/api/infrastructure/adapters-common.md
                            -   "Observability": 04-reference/api/infrastructure/observability.md
                            -   "Storage": 04-reference/api/infrastructure/storage.md
                            -   "Unified HTTP Client": 04-reference/api/infrastructure/unified-http-client.md
                    -   Composition:
                            -   "Composition API": 04-reference/api/composition.md
                            -   "Bootstrap": 04-reference/api/composition/bootstrap.md
                            -   "Factories": 04-reference/api/composition/factories.md
            -   Schemas:
                    -   "Activity Schema": 04-reference/schemas/domain/chembl/activity-schema.md
                    -   "Assay Schema": 04-reference/schemas/domain/chembl/assay-schema.md
                    -   "Molecule Schema": 04-reference/schemas/domain/chembl/molecule-schema.md
                    -   "Target Schema": 04-reference/schemas/domain/chembl/target-schema.md
    -   Operations:
            -   Overview: 05-operations/README.md
            -   Runbooks:
                    -   "Index": 05-operations/runbooks/index.md
                    -   "Pipeline Failure (Critical)": 05-operations/runbooks/pipeline-failure-critical.md
                    -   "Pipeline Failure (Recovery)": 05-operations/runbooks/pipeline-failure-recovery.md
                    -   "Pipeline Failure (DQ)": 05-operations/runbooks/pipeline-failure-dq.md
                    -   "DQ Failure Investigation": 05-operations/runbooks/dq-failure-investigation.md
                    -   "Data Recovery": 05-operations/runbooks/data-recovery.md
                    -   "Incident Response": 05-operations/runbooks/incident-response.md
                    -   "Backfill & Rebuild": 05-operations/runbooks/backfill-rebuild.md
                    -   "Checkpoint Debugging": 05-operations/runbooks/checkpoint-debugging.md
                    -   "Schema Evolution": 05-operations/runbooks/schema-evolution.md
                    -   "Stale Lock": 05-operations/runbooks/stale-lock.md
                    -   "Quarantine Management": 05-operations/runbooks/quarantine-management.md
                    -   "VACUUM Procedures": 05-operations/runbooks/vacuum-procedures.md
                    -   "Observability Checklist": 05-operations/runbooks/observability-checklist.md
                    -   "Run Manifest Inspection": 05-operations/runbooks/run-manifest-inspection.md
                    -   "Traceability Signal Ownership": 05-operations/runbooks/traceability-signal-ownership.md
                    -   "Traceability Tabletop Drills": 05-operations/runbooks/traceability-tabletop-drills.md
                    -   "Traceability Adoption Checklist": 05-operations/runbooks/traceability-adoption-checklist.md
                    -   "Traceability Wave 5 Closeout Pack": 05-operations/runbooks/traceability-wave5-closeout-pack.md
                    -   "Scaling": 05-operations/runbooks/scaling.md
                    -   "Publication Validation": 05-operations/runbooks/publication-validation-runbook.md
            -   "Performance Baselines": 05-operations/performance-baselines.md
            -   "VACUUM & Retention": 05-operations/vacuum-retention.md
    -   "Internal / Extended":
            -   Agents:
                    -   "Agents Overview": 00-project/ai/agents/README.md
                    -   "AGENT": 00-project/ai/agents/guides/AGENT.md
                    -   "CLAUDE": 00-project/ai/agents/guides/CLAUDE.md
                    -   "CODEX": 00-project/ai/agents/guides/CODEX.md
                    -   "GEMINI": 00-project/ai/agents/guides/GEMINI.md
                    -   "Profiles Catalog": 00-project/ai/agents/agents/README.md
                    -   "Agent Orchestration Rules": 00-project/ai/agents/policy/agent-orchestration-rules.md
                    -   "Agent Naming Policy and Rename Plan (2026-03-08)": 00-project/ai/agents/policy/AGENT_NAMING_POLICY_AND_RENAME_PLAN_2026-03-08.md
                    -   "Consolidation Validation": 00-project/ai/agents/policy/CONSOLIDATION_VALIDATION.md
                    -   "Agent Consolidation Matrix (2026-03-08)": 00-project/ai/agents/policy/AGENT_CONSOLIDATION_MATRIX_2026-03-08.md
                    -   "Collected Prompts Index": 00-project/ai/prompts/COLLECTED_PROMPTS_INDEX.md
                    -   "Shared Agent Memory": 00-project/ai/memory/agent-memory.md
                    -   "Agent Memory": 00-project/ai/agents/runtime/agent-memory.md
                    -   "QA Orchestrator Prompt": 00-project/ai/agents/runtime/py-qa-orchestrator.md
                    -   "Orchestration": 00-project/ai/agents/agents/ORCHESTRATION.md
            -   "Project Architecture Index": 00-project/architecture-index.md
            -   "Legacy Documentation Index": INDEX.md
            -   "Architecture Extras":
                    -   "Compatibility Facade Inventory": 02-architecture/07-compatibility-facade-inventory.md
                    -   "Compatibility Facade Snapshot": 02-architecture/07-compatibility-facade-snapshot.md
                    -   "Diagram Policy (Canonical)": 02-architecture/diagrams/governance/policy.md
                    -   "Diagram Policy (Historical)": 02-architecture/diagrams/governance/00-diagramming-policy.md
                    -   "Architecture Diagrams (Legacy Index)": 02-architecture/diagrams/guide/architecture-reference.md
                    -   "Diagram Root README": 02-architecture/diagrams/README.md
                    -   "Class Diagram Description Overview": 02-architecture/diagrams/descriptions/class-summary.md
                    -   "Architecture Bundle": 02-architecture/diagrams/bundles/architecture.bundle.md
                    -   "Foundation Bundle": 02-architecture/diagrams/bundles/foundation.bundle.md
                    -   "Class Bundle": 02-architecture/diagrams/bundles/class.bundle.md
                    -   "Views Bundle": 02-architecture/diagrams/bundles/views.bundle.md
                    -   "Rendered Diagram Indexes":
                            -   "Architecture SVG Index": 02-architecture/diagrams/architecture/svg/INDEX.md
                            -   "Architecture PNG Index": 02-architecture/diagrams/architecture/png/INDEX.md
                            -   "Class Diagram SVG Index": 02-architecture/diagrams/class-diagrams/svg/INDEX.md
                            -   "Class Diagram PNG Index": 02-architecture/diagrams/class-diagrams/png/INDEX.md
                            -   "Foundation SVG Index": 02-architecture/diagrams/foundation/svg/INDEX.md
                            -   "Foundation PNG Index": 02-architecture/diagrams/foundation/png/INDEX.md
                            -   "Views SVG Index": 02-architecture/diagrams/views/svg/INDEX.md
                            -   "Views PNG Index": 02-architecture/diagrams/views/png/INDEX.md
                    -   "Diagram Views Plan": 02-architecture/diagrams/governance/diagram-views-plan.md
                    -   "Diagram Prompt Expansion": 02-architecture/diagrams/governance/PROMPT-diagram-expansion.md
                    -   "Module Consolidation Requirements": 02-architecture/module-consolidation-migration-requirements.md
                    -   "Compatibility Facade Review History": 02-architecture/history/compatibility-facade-review-history.md
                    -   "Content Hash Policy": 02-architecture/policies/content-hash-identity-policy.md
            -   "Guide Extras":
                    -   "Silver Schema Testing Guide": 03-guides/silver-schema-testing-guide.md
            -   "Reference Extras":
                    -   "Contracts README": 04-reference/contracts/README.md
                    -   "Configuration Runtime Artifacts": 04-reference/components/config-runtime-artifacts.md
                    -   "DQ Contract System": 04-reference/components/dq-contract-system.md
                    -   "Hash Policy": 04-reference/hash-policy.md
                    -   "Publication Fields Reference": 04-reference/publication-fields-reference.md
                    -   "Publication Validation Index": 04-reference/publication-validation-index.md
                    -   "Composite Validation Layer": 04-reference/components/composite-validation-layer.md
                    -   "Composite Validation Service": 04-reference/components/composite-validation-service.md
                    -   "Phased Migration Support": 04-reference/components/phased-migration.md
                    -   "Pipeline Review Checklist": 04-reference/templates/pipeline-review-checklist.md
                    -   "Pipeline Legacy: ChEMBL Activity": 04-reference/pipelines/chembl-activity.md
                    -   "Pipeline Legacy: ChEMBL Assay": 04-reference/pipelines/chembl-assay.md
                    -   "Pipeline Legacy: OpenAlex Publication": 04-reference/pipelines/openalex/01-publication-spec.md
                    -   "Pipeline Legacy: SemanticScholar Publication": 04-reference/pipelines/semanticscholar/01-publication-spec.md
            -   "Operations Extras":
                    -   "Monitoring Guide": 05-operations/01-monitoring-guide.md
                    -   "Deployment & Tooling Extras":
                            -   "Overview": 05-operations/deployment/README.md
                            -   "Experimental Kubernetes":
                                    -   "Guide": 05-operations/deployment/deployment-guide.md
                                    -   "Summary": 05-operations/deployment/k8s-summary.md
                            -   "Auxiliary Neo4j / MCP Tooling":
                                    -   "Neo4j Memory Setup": 05-operations/deployment/neo4j-memory-setup.md
                                    -   "MCP Neo4j Memory Summary": 05-operations/deployment/mcp-neo4j-memory-summary.md
                    -   "Historical Verification & Release Evidence":
                            -   "Operations Archive Index": 05-operations/archive-index.md
                            -   "Release Checklist (v5.9)": 05-operations/release-checklist.md
                            -   "Endpoint Validation Checklist": 05-operations/verification/endpoint-validation-checklist.md
                            -   "VCR Provider Rebalancing": 05-operations/verification/vcr-provider-rebalancing.md
                            -   "VCR Test Tasks": 05-operations/verification/vcr-test-tasks.md
            -   "Diagram Descriptions":
                -   "Index": 02-architecture/diagrams/descriptions/INDEX.md
                -   "Legacy":
                    -   "01 Full System Component Full": 02-architecture/diagrams/descriptions/legacy/mermaid/01-full-system-component-full.md
                    -   "04 Domain Layer Class Diagram Full": 02-architecture/diagrams/descriptions/legacy/mermaid/04-domain-layer-class-diagram-full.md
                    -   "21 Activity Entity Data Flow Full": 02-architecture/diagrams/descriptions/legacy/mermaid/21-activity-entity-data-flow-full.md
                    -   "26 Hexagonal Ports Adapters Full": 02-architecture/diagrams/descriptions/legacy/mermaid/26-hexagonal-ports-adapters-full.md
                    -   "28 Composition Root Di Graph Full": 02-architecture/diagrams/descriptions/legacy/mermaid/28-composition-root-di-graph-full.md
                    -   "29 Composite Pipeline Workflow Full": 02-architecture/diagrams/descriptions/legacy/mermaid/29-composite-pipeline-workflow-full.md
                    -   "30 Port Adapter Mapping Full": 02-architecture/diagrams/descriptions/legacy/mermaid/30-port-adapter-mapping-full.md
                    -   "32 Single Record Journey Full": 02-architecture/diagrams/descriptions/legacy/mermaid/32-single-record-journey-full.md
                    -   "35 Bootstrap Sequence Full": 02-architecture/diagrams/descriptions/legacy/mermaid/35-bootstrap-sequence-full.md
                    -   "39 Medallion Invariants Full": 02-architecture/diagrams/descriptions/legacy/mermaid/39-medallion-invariants-full.md
                    -   "44 Cross Provider Enrichment Full": 02-architecture/diagrams/descriptions/legacy/mermaid/44-cross-provider-enrichment-full.md
                    -   "46 Yaml Config Resolution Full": 02-architecture/diagrams/descriptions/legacy/mermaid/46-yaml-config-resolution-full.md
                -   "Architecture":
                    -   "01 High Level Hexagonal": 02-architecture/diagrams/descriptions/architecture/01-high-level-hexagonal.md
                    -   "01A Hexagonal Overview": 02-architecture/diagrams/descriptions/architecture/01a-hexagonal-overview.md
                    -   "01B Hexagonal Domain App": 02-architecture/diagrams/descriptions/architecture/01b-hexagonal-domain-app.md
                    -   "01C Hexagonal Infra Comp": 02-architecture/diagrams/descriptions/architecture/01c-hexagonal-infra-comp.md
                    -   "01D Hexagonal Overview Rounded": 02-architecture/diagrams/descriptions/architecture/01d-hexagonal-overview-rounded.md
                    -   "02 Layer Dependency Matrix": 02-architecture/diagrams/descriptions/architecture/02-layer-dependency-matrix.md
                    -   "03 Medallion Data Flow": 02-architecture/diagrams/descriptions/architecture/03-medallion-data-flow.md
                    -   "03A Medallion Layers Overview": 02-architecture/diagrams/descriptions/architecture/03a-medallion-layers-overview.md
                    -   "04 Pipeline Execution Flow": 02-architecture/diagrams/descriptions/architecture/04-pipeline-execution-flow.md
                    -   "05 Provider Adapter Hierarchy": 02-architecture/diagrams/descriptions/architecture/05-provider-adapter-hierarchy.md
                    -   "05A Adapter Hierarchy Base": 02-architecture/diagrams/descriptions/architecture/05a-adapter-hierarchy-base.md
                    -   "05B Adapter Hierarchy Providers": 02-architecture/diagrams/descriptions/architecture/05b-adapter-hierarchy-providers.md
                    -   "06 Storage Layer": 02-architecture/diagrams/descriptions/architecture/06-storage-layer.md
                    -   "06A Storage Writers": 02-architecture/diagrams/descriptions/architecture/06a-storage-writers.md
                    -   "06B Storage Support": 02-architecture/diagrams/descriptions/architecture/06b-storage-support.md
                    -   "07 Dq System": 02-architecture/diagrams/descriptions/architecture/07-dq-system.md
                    -   "07A Dq Analysis": 02-architecture/diagrams/descriptions/architecture/07a-dq-analysis.md
                    -   "07B Dq Pipeline": 02-architecture/diagrams/descriptions/architecture/07b-dq-pipeline.md
                    -   "08 Composite Pipeline": 02-architecture/diagrams/descriptions/architecture/08-composite-pipeline.md
                    -   "08A Composite Config": 02-architecture/diagrams/descriptions/architecture/08a-composite-config.md
                    -   "08B Composite Execution": 02-architecture/diagrams/descriptions/architecture/08b-composite-execution.md
                    -   "09 Observability Stack": 02-architecture/diagrams/descriptions/architecture/09-observability-stack.md
                    -   "09A Observability App": 02-architecture/diagrams/descriptions/architecture/09a-observability-app.md
                    -   "09B Observability Infra": 02-architecture/diagrams/descriptions/architecture/09b-observability-infra.md
                    -   "10 Resilience Patterns": 02-architecture/diagrams/descriptions/architecture/10-resilience-patterns.md
                    -   "11 Configuration System": 02-architecture/diagrams/descriptions/architecture/11-configuration-system.md
                    -   "11A Config Loading": 02-architecture/diagrams/descriptions/architecture/11a-config-loading.md
                    -   "11B Config Domain": 02-architecture/diagrams/descriptions/architecture/11b-config-domain.md
                    -   "12 Bootstrap Di Container": 02-architecture/diagrams/descriptions/architecture/12-bootstrap-di-container.md
                    -   "12A Bootstrap Factories": 02-architecture/diagrams/descriptions/architecture/12a-bootstrap-factories.md
                    -   "12B Bootstrap Wiring": 02-architecture/diagrams/descriptions/architecture/12b-bootstrap-wiring.md
                    -   "13 Port Protocol Contracts": 02-architecture/diagrams/descriptions/architecture/13-port-protocol-contracts.md
                    -   "13A Data Storage Ports": 02-architecture/diagrams/descriptions/architecture/13a-data-storage-ports.md
                    -   "13A Port Contracts Data Sources": 02-architecture/diagrams/descriptions/architecture/13a-port-contracts-data-sources.md
                    -   "13B Operational Ports": 02-architecture/diagrams/descriptions/architecture/13b-operational-ports.md
                    -   "13B Port Contracts Storage": 02-architecture/diagrams/descriptions/architecture/13b-port-contracts-storage.md
                    -   "13C Port Contracts Observability": 02-architecture/diagrams/descriptions/architecture/13c-port-contracts-observability.md
                    -   "13C Validation Dq Ports": 02-architecture/diagrams/descriptions/architecture/13c-validation-dq-ports.md
                    -   "13D Port Contracts Services": 02-architecture/diagrams/descriptions/architecture/13d-port-contracts-services.md
                    -   "13E Operational Ports Domain": 02-architecture/diagrams/descriptions/architecture/13e-operational-ports-domain.md
                    -   "13F Operational Ports Infra": 02-architecture/diagrams/descriptions/architecture/13f-operational-ports-infra.md
                    -   "14 Cli Interface Layer": 02-architecture/diagrams/descriptions/architecture/14-cli-interface-layer.md
                    -   "14A Cli Commands": 02-architecture/diagrams/descriptions/architecture/14a-cli-commands.md
                    -   "14B Cli Routing": 02-architecture/diagrams/descriptions/architecture/14b-cli-routing.md
                    -   "15 Batch Executor Internals": 02-architecture/diagrams/descriptions/architecture/15-batch-executor-internals.md
                    -   "16 Transformer Hierarchy": 02-architecture/diagrams/descriptions/architecture/16-transformer-hierarchy.md
                    -   "16A Transformer Base": 02-architecture/diagrams/descriptions/architecture/16a-transformer-base.md
                    -   "16B Transformer Pub Other": 02-architecture/diagrams/descriptions/architecture/16b-transformer-pub-other.md
                    -   "17 Security Pii Audit": 02-architecture/diagrams/descriptions/architecture/17-security-pii-audit.md
                    -   "18 Lock Checkpoint Shutdown": 02-architecture/diagrams/descriptions/architecture/18-lock-checkpoint-shutdown.md
                    -   "18A Lock System": 02-architecture/diagrams/descriptions/architecture/18a-lock-system.md
                    -   "18B Checkpoint Shutdown": 02-architecture/diagrams/descriptions/architecture/18b-checkpoint-shutdown.md
                    -   "Control Plane & Runtime":
                            -   "19 Control Plane Artifacts": 02-architecture/diagrams/descriptions/architecture/19-control-plane-artifacts.md
                            -   "20 Data Traceability Runtime": 02-architecture/diagrams/descriptions/architecture/20-data-traceability-runtime.md
                            -   "21 Idempotent Processing Guards": 02-architecture/diagrams/descriptions/architecture/21-idempotent-processing-guards.md
                            -   "22 Data Operations Observability": 02-architecture/diagrams/descriptions/architecture/22-data-operations-observability.md
                            -   "23 Reproducible Run Contract": 02-architecture/diagrams/descriptions/architecture/23-reproducible-run-contract.md
                -   "Class Diagrams":
                    -   "Index": 02-architecture/diagrams/descriptions/class/INDEX.md
                    -   "01 Domain Ports": 02-architecture/diagrams/descriptions/class/01-domain-ports.md
                    -   "02 Entities Aggregates": 02-architecture/diagrams/descriptions/class/02-entities-aggregates.md
                    -   "03 Value Objects": 02-architecture/diagrams/descriptions/class/03-value-objects.md
                    -   "04 Types Enums": 02-architecture/diagrams/descriptions/class/04-types-enums.md
                    -   "05 Exceptions": 02-architecture/diagrams/descriptions/class/05-exceptions.md
                    -   "06 Config Classes": 02-architecture/diagrams/descriptions/class/06-config-classes.md
                    -   "07 Application Core Services": 02-architecture/diagrams/descriptions/class/07-application-core-services.md
                    -   "08 Application Services": 02-architecture/diagrams/descriptions/class/08-application-services.md
                    -   "09 Transformers": 02-architecture/diagrams/descriptions/class/09-transformers.md
                    -   "10 Adapters": 02-architecture/diagrams/descriptions/class/10-adapters.md
                    -   "11 Storage": 02-architecture/diagrams/descriptions/class/11-storage.md
                    -   "12 Composite Pipeline": 02-architecture/diagrams/descriptions/class/12-composite-pipeline.md
                    -   "13 Domain Services": 02-architecture/diagrams/descriptions/class/13-domain-services.md
                    -   "14 Observability": 02-architecture/diagrams/descriptions/class/14-observability.md
                    -   "15 Extractors": 02-architecture/diagrams/descriptions/class/15-extractors.md
                    -   "16 Factories Bootstrap": 02-architecture/diagrams/descriptions/class/16-factories-bootstrap.md
                -   "Foundation":
                    -   "01 Full System Component": 02-architecture/diagrams/descriptions/foundation/01-full-system-component.md
                    -   "01 High Level": 02-architecture/diagrams/descriptions/foundation/01-high-level.md
                    -   "02 Full Medallion Data Flow": 02-architecture/diagrams/descriptions/foundation/02-full-medallion-data-flow.md
                    -   "03 Pipeline Execution Happy Path": 02-architecture/diagrams/descriptions/foundation/03-pipeline-execution-happy-path.md
                    -   "04 Domain Layer Class Diagram": 02-architecture/diagrams/descriptions/foundation/04-domain-layer-class-diagram.md
                    -   "04 Error Flow": 02-architecture/diagrams/descriptions/foundation/04-error-flow.md
                    -   "05 Layers Interaction": 02-architecture/diagrams/descriptions/foundation/05-layers-interaction.md
                    -   "05 Pipeline Lifecycle States": 02-architecture/diagrams/descriptions/foundation/05-pipeline-lifecycle-states.md
                    -   "06 Application Layer Class Diagram": 02-architecture/diagrams/descriptions/foundation/06-application-layer-class-diagram.md
                    -   "06 Pipeline Execution": 02-architecture/diagrams/descriptions/foundation/06-pipeline-execution.md
                    -   "07 Circuit Breaker States": 02-architecture/diagrams/descriptions/foundation/07-circuit-breaker-states.md
                    -   "07 Medallion Flow": 02-architecture/diagrams/descriptions/foundation/07-medallion-flow.md
                    -   "08 Complete Etl Workflow": 02-architecture/diagrams/descriptions/foundation/08-complete-etl-workflow.md
                    -   "08 Domain Ddd": 02-architecture/diagrams/descriptions/foundation/08-domain-ddd.md
                    -   "09 Full Er Diagram": 02-architecture/diagrams/descriptions/foundation/09-full-er-diagram.md
                    -   "10 Infrastructure Layer Class Diagram": 02-architecture/diagrams/descriptions/foundation/10-infrastructure-layer-class-diagram.md
                    -   "11 Lock Acquisition Sequence": 02-architecture/diagrams/descriptions/foundation/11-lock-acquisition-sequence.md
                    -   "12 Local Deployment Architecture": 02-architecture/diagrams/descriptions/foundation/12-local-deployment-architecture.md
                    -   "13 Domain Models Relationship": 02-architecture/diagrams/descriptions/foundation/13-domain-models-relationship.md
                    -   "14 Provider Health States": 02-architecture/diagrams/descriptions/foundation/14-provider-health-states.md
                    -   "15 Dq Check Workflow": 02-architecture/diagrams/descriptions/foundation/15-dq-check-workflow.md
                    -   "16 Memory Lock Class": 02-architecture/diagrams/descriptions/foundation/16-memory-lock-class.md
                    -   "17 Pipeline Hierarchy": 02-architecture/diagrams/descriptions/foundation/17-pipeline-hierarchy.md
                    -   "18 Bronze Write Sequence": 02-architecture/diagrams/descriptions/foundation/18-bronze-write-sequence.md
                    -   "19 Delta Lake Write Sequence": 02-architecture/diagrams/descriptions/foundation/19-delta-lake-write-sequence.md
                    -   "20 Quarantine Record States": 02-architecture/diagrams/descriptions/foundation/20-quarantine-record-states.md
                    -   "21 Activity Entity Data Flow": 02-architecture/diagrams/descriptions/foundation/21-activity-entity-data-flow.md
                    -   "22 Client Api Request Sequence": 02-architecture/diagrams/descriptions/foundation/22-client-api-request-sequence.md
                    -   "23 Silver Writer Class": 02-architecture/diagrams/descriptions/foundation/23-silver-writer-class.md
                    -   "24 Hash Service Class": 02-architecture/diagrams/descriptions/foundation/24-hash-service-class.md
                    -   "25 Circuit Breaker Observer Class": 02-architecture/diagrams/descriptions/foundation/25-circuit-breaker-observer-class.md
                    -   "26 Hexagonal Ports Adapters": 02-architecture/diagrams/descriptions/foundation/26-hexagonal-ports-adapters.md
                    -   "27 Import Matrix Enforcement": 02-architecture/diagrams/descriptions/foundation/27-import-matrix-enforcement.md
                    -   "28 Composition Root Di Graph": 02-architecture/diagrams/descriptions/foundation/28-composition-root-di-graph.md
                    -   "29 Composite Pipeline Workflow": 02-architecture/diagrams/descriptions/foundation/29-composite-pipeline-workflow.md
                    -   "30 Port Adapter Mapping": 02-architecture/diagrams/descriptions/foundation/30-port-adapter-mapping.md
                    -   "31 Pipeline Run Lifecycle": 02-architecture/diagrams/descriptions/foundation/31-pipeline-run-lifecycle.md
                    -   "32 Single Record Journey": 02-architecture/diagrams/descriptions/foundation/32-single-record-journey.md
                    -   "33 Cli Run Interaction": 02-architecture/diagrams/descriptions/foundation/33-cli-run-interaction.md
                    -   "34 Batch Processing Flow": 02-architecture/diagrams/descriptions/foundation/34-batch-processing-flow.md
                    -   "36 Architecture Principles Mindmap": 02-architecture/diagrams/descriptions/foundation/36-architecture-principles-mindmap.md
                    -   "37 Cli Entry Full Chain": 02-architecture/diagrams/descriptions/foundation/37-cli-entry-full-chain.md
                    -   "38 Runtime Assembly Sequence": 02-architecture/diagrams/descriptions/foundation/38-runtime-assembly-sequence.md
                    -   "39 Medallion Invariants": 02-architecture/diagrams/descriptions/foundation/39-medallion-invariants.md
                    -   "40 Application Core Collaboration": 02-architecture/diagrams/descriptions/foundation/40-application-core-collaboration.md
                    -   "41 Error Classification Tree": 02-architecture/diagrams/descriptions/foundation/41-error-classification-tree.md
                    -   "42 Pipeline Runner Class": 02-architecture/diagrams/descriptions/foundation/42-pipeline-runner-class.md
                    -   "43 Fan Out Fan In Pattern": 02-architecture/diagrams/descriptions/foundation/43-fan-out-fan-in-pattern.md
                    -   "44 Cross Provider Enrichment": 02-architecture/diagrams/descriptions/foundation/44-cross-provider-enrichment.md
                    -   "46 Yaml Config Resolution": 02-architecture/diagrams/descriptions/foundation/46-yaml-config-resolution.md
                    -   "47 Publication Merge Sources": 02-architecture/diagrams/descriptions/foundation/47-publication-merge-sources.md
                    -   "48 Composite Phase Lifecycle": 02-architecture/diagrams/descriptions/foundation/48-composite-phase-lifecycle.md
                    -   "49 Composite Runner Class": 02-architecture/diagrams/descriptions/foundation/49-composite-runner-class.md
                    -   "50 Exception Hierarchy": 02-architecture/diagrams/descriptions/foundation/50-exception-hierarchy.md
                -   "Views":
                    -   "00 Legend": 02-architecture/diagrams/descriptions/views/00-legend.md
                    -   "01 Full System Component Dataflow": 02-architecture/diagrams/descriptions/views/01-full-system-component-dataflow.md
                    -   "01 Full System Component Domain": 02-architecture/diagrams/descriptions/views/01-full-system-component-domain.md
                    -   "01 Full System Component Full": 02-architecture/diagrams/descriptions/views/01-full-system-component-full.md
                    -   "01 Full System Component Infra": 02-architecture/diagrams/descriptions/views/01-full-system-component-infra.md
                    -   "01 Full System Component Overview": 02-architecture/diagrams/descriptions/views/01-full-system-component-overview.md
                    -   "01 High Level Dataflow": 02-architecture/diagrams/descriptions/views/01-high-level-dataflow.md
                    -   "01 High Level Domain": 02-architecture/diagrams/descriptions/views/01-high-level-domain.md
                    -   "01 High Level Full": 02-architecture/diagrams/descriptions/views/01-high-level-full.md
                    -   "01 High Level Infra": 02-architecture/diagrams/descriptions/views/01-high-level-infra.md
                    -   "01 High Level Overview": 02-architecture/diagrams/descriptions/views/01-high-level-overview.md
                    -   "02 Medallion Dataflow": 02-architecture/diagrams/descriptions/views/02-medallion-dataflow.md
                    -   "02 Medallion Domain": 02-architecture/diagrams/descriptions/views/02-medallion-domain.md
                    -   "02 Medallion Full": 02-architecture/diagrams/descriptions/views/02-medallion-full.md
                    -   "02 Medallion Infra": 02-architecture/diagrams/descriptions/views/02-medallion-infra.md
                    -   "02 Medallion Overview": 02-architecture/diagrams/descriptions/views/02-medallion-overview.md
                    -   "Focused Runtime Views":
                            -   "03 Medallion Data Flow Full": 02-architecture/diagrams/descriptions/views/03-medallion-data-flow-full.md
                            -   "03 Medallion Data Flow Overview": 02-architecture/diagrams/descriptions/views/03-medallion-data-flow-overview.md
                            -   "13 Port Protocol Contracts Full": 02-architecture/diagrams/descriptions/views/13-port-protocol-contracts-full.md
                            -   "13 Port Protocol Contracts Overview": 02-architecture/diagrams/descriptions/views/13-port-protocol-contracts-overview.md
                            -   "16 Transformer Hierarchy Full": 02-architecture/diagrams/descriptions/views/16-transformer-hierarchy-full.md
                            -   "16 Transformer Hierarchy Overview": 02-architecture/diagrams/descriptions/views/16-transformer-hierarchy-overview.md
                            -   "21 Idempotent Processing Guards Overview": 02-architecture/diagrams/descriptions/views/21-idempotent-processing-guards-overview.md
                            -   "23 Reproducible Run Contract Overview": 02-architecture/diagrams/descriptions/views/23-reproducible-run-contract-overview.md
                            -   "24 Data Runtime Quality Map Overview": 02-architecture/diagrams/descriptions/views/24-data-runtime-quality-map-overview.md
                    -   "04 Domain Layer Class Diagram Dataflow": 02-architecture/diagrams/descriptions/views/04-domain-layer-class-diagram-dataflow.md
                    -   "04 Domain Layer Class Diagram Domain": 02-architecture/diagrams/descriptions/views/04-domain-layer-class-diagram-domain.md
                    -   "04 Domain Layer Class Diagram Full": 02-architecture/diagrams/descriptions/views/04-domain-layer-class-diagram-full.md
                    -   "04 Domain Layer Class Diagram Infra": 02-architecture/diagrams/descriptions/views/04-domain-layer-class-diagram-infra.md
                    -   "04 Domain Layer Class Diagram Overview": 02-architecture/diagrams/descriptions/views/04-domain-layer-class-diagram-overview.md
                    -   "05 Layers Interaction Dataflow": 02-architecture/diagrams/descriptions/views/05-layers-interaction-dataflow.md
                    -   "05 Layers Interaction Domain": 02-architecture/diagrams/descriptions/views/05-layers-interaction-domain.md
                    -   "05 Layers Interaction Full": 02-architecture/diagrams/descriptions/views/05-layers-interaction-full.md
                    -   "05 Layers Interaction Infra": 02-architecture/diagrams/descriptions/views/05-layers-interaction-infra.md
                    -   "05 Layers Interaction Overview": 02-architecture/diagrams/descriptions/views/05-layers-interaction-overview.md
                    -   "05 Pipeline Lifecycle States Dataflow": 02-architecture/diagrams/descriptions/views/05-pipeline-lifecycle-states-dataflow.md
                    -   "05 Pipeline Lifecycle States Domain": 02-architecture/diagrams/descriptions/views/05-pipeline-lifecycle-states-domain.md
                    -   "05 Pipeline Lifecycle States Full": 02-architecture/diagrams/descriptions/views/05-pipeline-lifecycle-states-full.md
                    -   "05 Pipeline Lifecycle States Infra": 02-architecture/diagrams/descriptions/views/05-pipeline-lifecycle-states-infra.md
                    -   "05 Pipeline Lifecycle States Overview": 02-architecture/diagrams/descriptions/views/05-pipeline-lifecycle-states-overview.md
                    -   "06 Application Layer Class Diagram Dataflow": 02-architecture/diagrams/descriptions/views/06-application-layer-class-diagram-dataflow.md
                    -   "06 Application Layer Class Diagram Domain": 02-architecture/diagrams/descriptions/views/06-application-layer-class-diagram-domain.md
                    -   "06 Application Layer Class Diagram Full": 02-architecture/diagrams/descriptions/views/06-application-layer-class-diagram-full.md
                    -   "06 Application Layer Class Diagram Infra": 02-architecture/diagrams/descriptions/views/06-application-layer-class-diagram-infra.md
                    -   "06 Application Layer Class Diagram Overview": 02-architecture/diagrams/descriptions/views/06-application-layer-class-diagram-overview.md
                    -   "07 Circuit Breaker States Dataflow": 02-architecture/diagrams/descriptions/views/07-circuit-breaker-states-dataflow.md
                    -   "07 Circuit Breaker States Domain": 02-architecture/diagrams/descriptions/views/07-circuit-breaker-states-domain.md
                    -   "07 Circuit Breaker States Full": 02-architecture/diagrams/descriptions/views/07-circuit-breaker-states-full.md
                    -   "07 Circuit Breaker States Infra": 02-architecture/diagrams/descriptions/views/07-circuit-breaker-states-infra.md
                    -   "07 Circuit Breaker States Overview": 02-architecture/diagrams/descriptions/views/07-circuit-breaker-states-overview.md
                    -   "08 Complete Etl Workflow Dataflow": 02-architecture/diagrams/descriptions/views/08-complete-etl-workflow-dataflow.md
                    -   "08 Complete Etl Workflow Domain": 02-architecture/diagrams/descriptions/views/08-complete-etl-workflow-domain.md
                    -   "08 Complete Etl Workflow Full": 02-architecture/diagrams/descriptions/views/08-complete-etl-workflow-full.md
                    -   "08 Complete Etl Workflow Infra": 02-architecture/diagrams/descriptions/views/08-complete-etl-workflow-infra.md
                    -   "08 Complete Etl Workflow Overview": 02-architecture/diagrams/descriptions/views/08-complete-etl-workflow-overview.md
                    -   "08 Domain Ddd Dataflow": 02-architecture/diagrams/descriptions/views/08-domain-ddd-dataflow.md
                    -   "08 Domain Ddd Domain": 02-architecture/diagrams/descriptions/views/08-domain-ddd-domain.md
                    -   "08 Domain Ddd Full": 02-architecture/diagrams/descriptions/views/08-domain-ddd-full.md
                    -   "08 Domain Ddd Infra": 02-architecture/diagrams/descriptions/views/08-domain-ddd-infra.md
                    -   "08 Domain Ddd Overview": 02-architecture/diagrams/descriptions/views/08-domain-ddd-overview.md
                    -   "10 Infrastructure Layer Class Diagram Dataflow": 02-architecture/diagrams/descriptions/views/10-infrastructure-layer-class-diagram-dataflow.md
                    -   "10 Infrastructure Layer Class Diagram Domain": 02-architecture/diagrams/descriptions/views/10-infrastructure-layer-class-diagram-domain.md
                    -   "10 Infrastructure Layer Class Diagram Full": 02-architecture/diagrams/descriptions/views/10-infrastructure-layer-class-diagram-full.md
                    -   "10 Infrastructure Layer Class Diagram Infra": 02-architecture/diagrams/descriptions/views/10-infrastructure-layer-class-diagram-infra.md
                    -   "10 Infrastructure Layer Class Diagram Overview": 02-architecture/diagrams/descriptions/views/10-infrastructure-layer-class-diagram-overview.md
                    -   "12 Local Deployment Architecture Dataflow": 02-architecture/diagrams/descriptions/views/12-local-deployment-architecture-dataflow.md
                    -   "12 Local Deployment Architecture Domain": 02-architecture/diagrams/descriptions/views/12-local-deployment-architecture-domain.md
                    -   "12 Local Deployment Architecture Full": 02-architecture/diagrams/descriptions/views/12-local-deployment-architecture-full.md
                    -   "12 Local Deployment Architecture Infra": 02-architecture/diagrams/descriptions/views/12-local-deployment-architecture-infra.md
                    -   "12 Local Deployment Architecture Overview": 02-architecture/diagrams/descriptions/views/12-local-deployment-architecture-overview.md
                    -   "14 Provider Health States Dataflow": 02-architecture/diagrams/descriptions/views/14-provider-health-states-dataflow.md
                    -   "14 Provider Health States Domain": 02-architecture/diagrams/descriptions/views/14-provider-health-states-domain.md
                    -   "14 Provider Health States Full": 02-architecture/diagrams/descriptions/views/14-provider-health-states-full.md
                    -   "14 Provider Health States Infra": 02-architecture/diagrams/descriptions/views/14-provider-health-states-infra.md
                    -   "14 Provider Health States Overview": 02-architecture/diagrams/descriptions/views/14-provider-health-states-overview.md
                    -   "15 Dq Check Workflow Dataflow": 02-architecture/diagrams/descriptions/views/15-dq-check-workflow-dataflow.md
                    -   "15 Dq Check Workflow Domain": 02-architecture/diagrams/descriptions/views/15-dq-check-workflow-domain.md
                    -   "15 Dq Check Workflow Full": 02-architecture/diagrams/descriptions/views/15-dq-check-workflow-full.md
                    -   "15 Dq Check Workflow Infra": 02-architecture/diagrams/descriptions/views/15-dq-check-workflow-infra.md
                    -   "15 Dq Check Workflow Overview": 02-architecture/diagrams/descriptions/views/15-dq-check-workflow-overview.md
                    -   "21 Activity Entity Data Flow Dataflow": 02-architecture/diagrams/descriptions/views/21-activity-entity-data-flow-dataflow.md
                    -   "21 Activity Entity Data Flow Domain": 02-architecture/diagrams/descriptions/views/21-activity-entity-data-flow-domain.md
                    -   "21 Activity Entity Data Flow Full": 02-architecture/diagrams/descriptions/views/21-activity-entity-data-flow-full.md
                    -   "21 Activity Entity Data Flow Infra": 02-architecture/diagrams/descriptions/views/21-activity-entity-data-flow-infra.md
                    -   "21 Activity Entity Data Flow Overview": 02-architecture/diagrams/descriptions/views/21-activity-entity-data-flow-overview.md
                    -   "26 Hexagonal Ports Adapters Dataflow": 02-architecture/diagrams/descriptions/views/26-hexagonal-ports-adapters-dataflow.md
                    -   "26 Hexagonal Ports Adapters Domain": 02-architecture/diagrams/descriptions/views/26-hexagonal-ports-adapters-domain.md
                    -   "26 Hexagonal Ports Adapters Full": 02-architecture/diagrams/descriptions/views/26-hexagonal-ports-adapters-full.md
                    -   "26 Hexagonal Ports Adapters Infra": 02-architecture/diagrams/descriptions/views/26-hexagonal-ports-adapters-infra.md
                    -   "26 Hexagonal Ports Adapters Overview": 02-architecture/diagrams/descriptions/views/26-hexagonal-ports-adapters-overview.md
                    -   "28 Composition Root Di Graph Dataflow": 02-architecture/diagrams/descriptions/views/28-composition-root-di-graph-dataflow.md
                    -   "28 Composition Root Di Graph Domain": 02-architecture/diagrams/descriptions/views/28-composition-root-di-graph-domain.md
                    -   "28 Composition Root Di Graph Full": 02-architecture/diagrams/descriptions/views/28-composition-root-di-graph-full.md
                    -   "28 Composition Root Di Graph Infra": 02-architecture/diagrams/descriptions/views/28-composition-root-di-graph-infra.md
                    -   "28 Composition Root Di Graph Overview": 02-architecture/diagrams/descriptions/views/28-composition-root-di-graph-overview.md
                    -   "29 Composite Pipeline Workflow Dataflow": 02-architecture/diagrams/descriptions/views/29-composite-pipeline-workflow-dataflow.md
                    -   "29 Composite Pipeline Workflow Domain": 02-architecture/diagrams/descriptions/views/29-composite-pipeline-workflow-domain.md
                    -   "29 Composite Pipeline Workflow Full": 02-architecture/diagrams/descriptions/views/29-composite-pipeline-workflow-full.md
                    -   "29 Composite Pipeline Workflow Infra": 02-architecture/diagrams/descriptions/views/29-composite-pipeline-workflow-infra.md
                    -   "29 Composite Pipeline Workflow Overview": 02-architecture/diagrams/descriptions/views/29-composite-pipeline-workflow-overview.md
                    -   "30 Port Adapter Mapping Dataflow": 02-architecture/diagrams/descriptions/views/30-port-adapter-mapping-dataflow.md
                    -   "30 Port Adapter Mapping Domain": 02-architecture/diagrams/descriptions/views/30-port-adapter-mapping-domain.md
                    -   "30 Port Adapter Mapping Full": 02-architecture/diagrams/descriptions/views/30-port-adapter-mapping-full.md
                    -   "30 Port Adapter Mapping Infra": 02-architecture/diagrams/descriptions/views/30-port-adapter-mapping-infra.md
                    -   "30 Port Adapter Mapping Overview": 02-architecture/diagrams/descriptions/views/30-port-adapter-mapping-overview.md
                    -   "31 Pipeline Run Lifecycle Dataflow": 02-architecture/diagrams/descriptions/views/31-pipeline-run-lifecycle-dataflow.md
                    -   "31 Pipeline Run Lifecycle Domain": 02-architecture/diagrams/descriptions/views/31-pipeline-run-lifecycle-domain.md
                    -   "31 Pipeline Run Lifecycle Full": 02-architecture/diagrams/descriptions/views/31-pipeline-run-lifecycle-full.md
                    -   "31 Pipeline Run Lifecycle Infra": 02-architecture/diagrams/descriptions/views/31-pipeline-run-lifecycle-infra.md
                    -   "31 Pipeline Run Lifecycle Overview": 02-architecture/diagrams/descriptions/views/31-pipeline-run-lifecycle-overview.md
                    -   "32 Single Record Journey Dataflow": 02-architecture/diagrams/descriptions/views/32-single-record-journey-dataflow.md
                    -   "32 Single Record Journey Domain": 02-architecture/diagrams/descriptions/views/32-single-record-journey-domain.md
                    -   "32 Single Record Journey Full": 02-architecture/diagrams/descriptions/views/32-single-record-journey-full.md
                    -   "32 Single Record Journey Infra": 02-architecture/diagrams/descriptions/views/32-single-record-journey-infra.md
                    -   "32 Single Record Journey Overview": 02-architecture/diagrams/descriptions/views/32-single-record-journey-overview.md
                    -   "33 Cli Run Interaction Dataflow": 02-architecture/diagrams/descriptions/views/33-cli-run-interaction-dataflow.md
                    -   "33 Cli Run Interaction Domain": 02-architecture/diagrams/descriptions/views/33-cli-run-interaction-domain.md
                    -   "33 Cli Run Interaction Full": 02-architecture/diagrams/descriptions/views/33-cli-run-interaction-full.md
                    -   "33 Cli Run Interaction Infra": 02-architecture/diagrams/descriptions/views/33-cli-run-interaction-infra.md
                    -   "33 Cli Run Interaction Overview": 02-architecture/diagrams/descriptions/views/33-cli-run-interaction-overview.md
                    -   "34 Batch Processing Flow Dataflow": 02-architecture/diagrams/descriptions/views/34-batch-processing-flow-dataflow.md
                    -   "34 Batch Processing Flow Domain": 02-architecture/diagrams/descriptions/views/34-batch-processing-flow-domain.md
                    -   "34 Batch Processing Flow Full": 02-architecture/diagrams/descriptions/views/34-batch-processing-flow-full.md
                    -   "34 Batch Processing Flow Infra": 02-architecture/diagrams/descriptions/views/34-batch-processing-flow-infra.md
                    -   "34 Batch Processing Flow Overview": 02-architecture/diagrams/descriptions/views/34-batch-processing-flow-overview.md
                    -   "35 Bootstrap Sequence Dataflow": 02-architecture/diagrams/descriptions/views/35-bootstrap-sequence-dataflow.md
                    -   "35 Bootstrap Sequence Domain": 02-architecture/diagrams/descriptions/views/35-bootstrap-sequence-domain.md
                    -   "35 Bootstrap Sequence Full": 02-architecture/diagrams/descriptions/views/35-bootstrap-sequence-full.md
                    -   "35 Bootstrap Sequence Infra": 02-architecture/diagrams/descriptions/views/35-bootstrap-sequence-infra.md
                    -   "35 Bootstrap Sequence Overview": 02-architecture/diagrams/descriptions/views/35-bootstrap-sequence-overview.md
                    -   "36 Architecture Principles Mindmap Dataflow": 02-architecture/diagrams/descriptions/views/36-architecture-principles-mindmap-dataflow.md
                    -   "36 Architecture Principles Mindmap Domain": 02-architecture/diagrams/descriptions/views/36-architecture-principles-mindmap-domain.md
                    -   "36 Architecture Principles Mindmap Full": 02-architecture/diagrams/descriptions/views/36-architecture-principles-mindmap-full.md
                    -   "36 Architecture Principles Mindmap Infra": 02-architecture/diagrams/descriptions/views/36-architecture-principles-mindmap-infra.md
                    -   "36 Architecture Principles Mindmap Overview": 02-architecture/diagrams/descriptions/views/36-architecture-principles-mindmap-overview.md
                    -   "39 Medallion Invariants Dataflow": 02-architecture/diagrams/descriptions/views/39-medallion-invariants-dataflow.md
                    -   "39 Medallion Invariants Domain": 02-architecture/diagrams/descriptions/views/39-medallion-invariants-domain.md
                    -   "39 Medallion Invariants Full": 02-architecture/diagrams/descriptions/views/39-medallion-invariants-full.md
                    -   "39 Medallion Invariants Infra": 02-architecture/diagrams/descriptions/views/39-medallion-invariants-infra.md
                    -   "39 Medallion Invariants Overview": 02-architecture/diagrams/descriptions/views/39-medallion-invariants-overview.md
                    -   "41 Error Classification Tree Dataflow": 02-architecture/diagrams/descriptions/views/41-error-classification-tree-dataflow.md
                    -   "41 Error Classification Tree Domain": 02-architecture/diagrams/descriptions/views/41-error-classification-tree-domain.md
                    -   "41 Error Classification Tree Full": 02-architecture/diagrams/descriptions/views/41-error-classification-tree-full.md
                    -   "41 Error Classification Tree Infra": 02-architecture/diagrams/descriptions/views/41-error-classification-tree-infra.md
                    -   "41 Error Classification Tree Overview": 02-architecture/diagrams/descriptions/views/41-error-classification-tree-overview.md
                    -   "44 Cross Provider Enrichment Dataflow": 02-architecture/diagrams/descriptions/views/44-cross-provider-enrichment-dataflow.md
                    -   "44 Cross Provider Enrichment Domain": 02-architecture/diagrams/descriptions/views/44-cross-provider-enrichment-domain.md
                    -   "44 Cross Provider Enrichment Full": 02-architecture/diagrams/descriptions/views/44-cross-provider-enrichment-full.md
                    -   "44 Cross Provider Enrichment Infra": 02-architecture/diagrams/descriptions/views/44-cross-provider-enrichment-infra.md
                    -   "44 Cross Provider Enrichment Overview": 02-architecture/diagrams/descriptions/views/44-cross-provider-enrichment-overview.md
                    -   "46 Yaml Config Resolution Dataflow": 02-architecture/diagrams/descriptions/views/46-yaml-config-resolution-dataflow.md
                    -   "46 Yaml Config Resolution Domain": 02-architecture/diagrams/descriptions/views/46-yaml-config-resolution-domain.md
                    -   "46 Yaml Config Resolution Full": 02-architecture/diagrams/descriptions/views/46-yaml-config-resolution-full.md
                    -   "46 Yaml Config Resolution Infra": 02-architecture/diagrams/descriptions/views/46-yaml-config-resolution-infra.md
                    -   "46 Yaml Config Resolution Overview": 02-architecture/diagrams/descriptions/views/46-yaml-config-resolution-overview.md
                    -   "48 Composite Phase Lifecycle Dataflow": 02-architecture/diagrams/descriptions/views/48-composite-phase-lifecycle-dataflow.md
                    -   "48 Composite Phase Lifecycle Domain": 02-architecture/diagrams/descriptions/views/48-composite-phase-lifecycle-domain.md
                    -   "48 Composite Phase Lifecycle Full": 02-architecture/diagrams/descriptions/views/48-composite-phase-lifecycle-full.md
                    -   "48 Composite Phase Lifecycle Infra": 02-architecture/diagrams/descriptions/views/48-composite-phase-lifecycle-infra.md
                    -   "48 Composite Phase Lifecycle Overview": 02-architecture/diagrams/descriptions/views/48-composite-phase-lifecycle-overview.md
                    -   "50 Exception Hierarchy Dataflow": 02-architecture/diagrams/descriptions/views/50-exception-hierarchy-dataflow.md
                    -   "50 Exception Hierarchy Domain": 02-architecture/diagrams/descriptions/views/50-exception-hierarchy-domain.md
                    -   "50 Exception Hierarchy Full": 02-architecture/diagrams/descriptions/views/50-exception-hierarchy-full.md
                    -   "50 Exception Hierarchy Infra": 02-architecture/diagrams/descriptions/views/50-exception-hierarchy-infra.md
                    -   "50 Exception Hierarchy Overview": 02-architecture/diagrams/descriptions/views/50-exception-hierarchy-overview.md
            -   "Diagram Programs":
                -   "Diagram Modernization Program": 02-architecture/diagrams/governance/diagram-modernization-program.md
                -   "Diagram Regression Test Plan": 02-architecture/diagrams/governance/diagram-regression-test-plan.md
            -   "Prompts":
                    -   "Diagram Docs Orchestrator Agent": 00-project/ai/agents/runtime/py-diagram-docs-orchestrator.md
            -   "Skills":
                -   "Overview": 00-project/ai/skills/README.md
                -   "Practical Index": 00-project/ai/skills/SKILLS-PRACTICAL-INDEX.md
                -   "Global Skills":
                    -   "Skill": 00-project/ai/skills/global/agent-orchestration/SKILL.md
                    -   "Skill": 00-project/ai/skills/global/documentation-audit/SKILL.md
                    -   "Audit Checklist": 00-project/ai/skills/global/documentation-audit/references/audit-checklist.md
                    -   "Report Template": 00-project/ai/skills/global/documentation-audit/references/report-template.md
                    -   "Skill": 00-project/ai/skills/global/gh-address-comments/SKILL.md
                    -   "Skill": 00-project/ai/skills/global/gh-fix-ci/SKILL.md
                    -   "Skill": 00-project/ai/skills/global/new-pipeline/SKILL.md
                    -   "Skill": 00-project/ai/skills/global/openai-docs/SKILL.md
                    -   "Skill": 00-project/ai/skills/global/public/architecture-guardian/SKILL.md
                    -   "Skill": 00-project/ai/skills/global/py-audit-bot/SKILL.md
                    -   "Legacy Skill py-code-bot": 00-project/ai/skills/global/py-code-bot/SKILL.md
                    -   "Skill": 00-project/ai/skills/global/py-config-bot/SKILL.md
                    -   "Skill": 00-project/ai/skills/global/py-debug-bot/SKILL.md
                    -   "Skill": 00-project/ai/skills/global/py-doc-bot/SKILL.md
                    -   "Skill": 00-project/ai/skills/global/py-plan-bot/SKILL.md
                    -   "Skill": 00-project/ai/skills/global/py-review-orchestrator/SKILL.md
                    -   "Skill": 00-project/ai/skills/global/py-test-bot/SKILL.md
                    -   "Skill": 00-project/ai/skills/global/vcr-record/SKILL.md
                    -   "Skill": 00-project/ai/skills/global/verify-architecture/SKILL.md
                -   "Local Skills":
                    -   "Skills Catalog": 00-project/ai/skills/local/SKILLS-CATALOG.md
                    -   "Skill": 00-project/ai/skills/local/agent-orchestration/SKILL.md
                    -   "Capability Discovery": 00-project/ai/skills/local/capability-discovery/SKILL.md
                    -   "Create PR": 00-project/ai/skills/local/create-pr/SKILL.md
                    -   "Deep Research": 00-project/ai/skills/local/deep-research/SKILL.md
                    -   "Evidence & Decisions":
                            -   "Collecting Evidence": 00-project/ai/skills/local/collecting-evidence/SKILL.md
                            -   "Hierarchical Evidence Orchestration": 00-project/ai/skills/local/hierarchical-evidence-orchestration/SKILL.md
                            -   "Synthesizing Pillars": 00-project/ai/skills/local/synthesizing-pillars/SKILL.md
                            -   "Making Decisions": 00-project/ai/skills/local/making-decisions/SKILL.md
                            -   "Generating Constrained Specs": 00-project/ai/skills/local/generating-constrained-specs/SKILL.md
                            -   "Initializing Ledger": 00-project/ai/skills/local/initializing-ledger/SKILL.md
                            -   "NCI Analysis": 00-project/ai/skills/local/nci-analysis/SKILL.md
                    -   "Deep Research Critique Framework": 00-project/ai/skills/local/deep-research/references/critique-framework.md
                    -   "Deep Research Report Templates": 00-project/ai/skills/local/deep-research/references/report-templates.md
                    -   "Deep Research Search Patterns": 00-project/ai/skills/local/deep-research/references/search-patterns.md
                    -   "Deep Research Source Evaluation": 00-project/ai/skills/local/deep-research/references/source-evaluation.md
                    -   "Skill": 00-project/ai/skills/local/documentation-audit/SKILL.md
                    -   "Audit Checklist": 00-project/ai/skills/local/documentation-audit/references/audit-checklist.md
                    -   "Report Template": 00-project/ai/skills/local/documentation-audit/references/report-template.md
                    -   "Skill": 00-project/ai/skills/local/documentation-cascade-audit/SKILL.md
                    -   "Skill": 00-project/ai/skills/local/new-pipeline/SKILL.md
                    -   "Skill": 00-project/ai/skills/local/public/architecture-guardian/SKILL.md
                    -   "Architecture Debt Bot": 00-project/ai/skills/local/py-architecture-debt-bot/SKILL.md
                    -   "Skill": 00-project/ai/skills/local/py-audit-bot/SKILL.md
                    -   "Legacy Skill py-code-bot": 00-project/ai/skills/local/py-code-bot/SKILL.md
                    -   "Skill": 00-project/ai/skills/local/py-config-bot/SKILL.md
                    -   "Skill": 00-project/ai/skills/local/py-debug-bot/SKILL.md
                    -   "Skill": 00-project/ai/skills/local/py-doc-bot/SKILL.md
                    -   "Skill": 00-project/ai/skills/local/py-plan-bot/SKILL.md
                    -   "Skill": 00-project/ai/skills/local/py-review-orchestrator/SKILL.md
                    -   "Skill": 00-project/ai/skills/local/py-test-bot/SKILL.md
                    -   "Skill": 00-project/ai/skills/local/py-test-swarm/SKILL.md
                    -   "Repo Config": 00-project/ai/skills/local/repo-config/SKILL.md
                    -   "Suggest Users": 00-project/ai/skills/local/suggest-users/SKILL.md
                    -   "L1 Playbook": 00-project/ai/skills/local/py-test-swarm/references/l1-playbook.md
                    -   "L2 L3 Task Brief": 00-project/ai/skills/local/py-test-swarm/references/l2-l3-task-brief.md
                    -   "Report Templates": 00-project/ai/skills/local/py-test-swarm/references/report-templates.md
                    -   "Telemetry And Flaky Db": 00-project/ai/skills/local/py-test-swarm/references/telemetry-and-flaky-db.md
                    -   "Skill": 00-project/ai/skills/local/technical-designer-mermaid/SKILL.md
                    -   "Patterns": 00-project/ai/skills/local/technical-designer-mermaid/references/patterns.md
                    -   "Skill": 00-project/ai/skills/local/vcr-record/SKILL.md
                    -   "Skill": 00-project/ai/skills/local/verify-architecture/SKILL.md