├── .actrc ├── .editorconfig ├── .gitattributes ├── .github ├── renovate.json5 └── workflows │ ├── ci.yml │ ├── docker-publish.yml │ ├── mcp-compliance.yml │ ├── pr-validation.yml │ └── renovate-config-validator.yml ├── .gitignore ├── .husky ├── pre-commit └── pre-push ├── CLAUDE.md ├── CONTRIBUTING.md ├── GEMINI.md ├── LICENSE ├── QWEN.md ├── README.md ├── assets └── logo.png ├── docs ├── DESIGN_DECISIONS.md ├── README.md ├── TODO.md ├── _generated │ ├── prompt_engine-params.md │ ├── prompt_manager-params.md │ └── system_control-params.md ├── architecture.md ├── chain-workflows.md ├── enhanced-gate-system.md ├── mcp-tooling-guide.md ├── operations-guide.md ├── prompt-authoring-guide.md └── release-notes.md ├── package.json ├── plans ├── file-size-plan │ ├── file-size-baseline.md │ └── file-size-enforcement-implementation.md ├── fix-mcp-package-installation.md ├── gates │ ├── gate-manager-implementation-roadmap.md │ ├── gate-updates │ │ ├── gate-enforcement-conductor.md │ │ ├── gate-retry-enforcement.md │ │ └── ❌gate-enforcement-system-deprecated.md │ └── ✅-shared-helpers-plan.md ├── lint-fix │ ├── LINT_FIX_STRATEGY.md │ ├── TECHNICAL_DEBT.md │ └── TYPESCRIPT_STYLE_GUIDE.md ├── mcp-package │ └── fix-npm-asset-distribution.md └── symbolic-gate-operator-enhancement.md ├── renovate.json └── server ├── .dependency-cruiser.cjs ├── .lintstagedrc.json ├── .prettierignore ├── .prettierrc.json ├── LICENSE ├── README.md ├── config.json ├── eslint-rules └── claude-plugin.js ├── eslint.config.js ├── gates ├── code-quality │ └── gate.yaml ├── content-structure │ └── gate.yaml ├── educational-clarity │ └── gate.yaml ├── framework-compliance │ └── gate.yaml ├── methodology-validation │ └── gate.yaml ├── research-quality │ └── gate.yaml ├── security-awareness │ └── gate.yaml └── technical-accuracy │ └── gate.yaml ├── graphs ├── execution-pipeline.dot ├── execution-pipeline.json ├── execution-pipeline.svg ├── frameworks.dot ├── frameworks.json ├── frameworks.svg ├── full-codebase.dot ├── full-codebase.json ├── full-codebase.svg ├── gates-system.dot ├── gates-system.json ├── gates-system.svg ├── mcp-tools.dot ├── mcp-tools.json ├── mcp-tools.svg ├── prompts-config.dot ├── prompts-config.json ├── prompts-config.svg ├── runtime-transports.dot ├── runtime-transports.json ├── runtime-transports.svg ├── semantic-analysis.dot ├── semantic-analysis.json └── semantic-analysis.svg ├── jest.config.cjs ├── methodologies ├── 5w1h │ ├── judge-prompt.md │ ├── methodology.yaml │ └── phases.yaml ├── cageerf │ ├── judge-prompt.md │ ├── methodology.yaml │ └── phases.yaml ├── react │ ├── judge-prompt.md │ ├── methodology.yaml │ └── phases.yaml └── scamper │ ├── judge-prompt.md │ ├── methodology.yaml │ └── phases.yaml ├── package-lock.json ├── package.json ├── plans └── injection-pipeline-fix │ └── IMPLEMENTATION_COMPLETE.md ├── prompts ├── analysis │ ├── content_analysis.md │ ├── deep_analysis.md │ ├── deep_research.md │ ├── markdown_notebook.md │ ├── note_integration.md │ ├── note_refinement.md │ ├── notes.md │ ├── progressive_research.md │ ├── prompts.json │ ├── query_refinement.md │ └── review.md ├── codebase-setup │ ├── codebase_protocol_init.md │ └── prompts.json ├── content_processing │ ├── obsidian_metadata_optimizer.md │ ├── prompts.json │ ├── vault_related_notes_finder.md │ └── video_notes_enhanced.md ├── debugging │ ├── analyze_logs.md │ └── prompts.json ├── development │ ├── code_review_optimization_chain.md │ ├── component_flow_analysis.md │ ├── create_modularization_plan.md │ ├── detect_code_issues.md │ ├── detect_project_commands.md │ ├── generate_comprehensive_claude_md.md │ ├── prompts.json │ ├── strategicImplement.md │ ├── suggest_code_improvements.md │ └── transform_code_to_modules.md ├── documentation │ ├── create_docs_chain.md │ ├── docs-content-creation.md │ ├── docs-content-planning.md │ ├── docs-final-assembly.md │ ├── docs-project-analysis.md │ ├── docs-review-refinement.md │ ├── prompts.json │ └── readme_improver.md ├── general │ ├── create_docs_chain.md │ ├── diagnose.md │ ├── hiring_manager_code_eval.md │ └── prompts.json ├── guidance │ ├── analytical.md │ ├── creative.md │ ├── procedural.md │ ├── prompts.json │ └── reasoning.md └── promptsConfig.json ├── scripts ├── generate-contracts.js ├── validate-filesize.js ├── validate-methodologies.js └── verify-action-inventory.js ├── src ├── .dockerignore ├── Dockerfile ├── api │ └── index.ts ├── chain-session │ ├── manager.ts │ ├── run-registry.ts │ └── types.ts ├── config │ └── index.ts ├── execution │ ├── context │ │ ├── context-resolver.ts │ │ ├── execution-context.ts │ │ ├── index.ts │ │ └── internal-state.ts │ ├── operators │ │ ├── chain-operator-executor.ts │ │ ├── index.ts │ │ └── types.ts │ ├── parsers │ │ ├── argument-parser.ts │ │ ├── argument-schema.ts │ │ ├── command-parser.ts │ │ ├── index.ts │ │ ├── parser-utils.ts │ │ ├── symbolic-operator-parser.ts │ │ └── types │ │ │ ├── command-parse-types.ts │ │ │ └── operator-types.ts │ ├── pipeline │ │ ├── criteria-guidance.ts │ │ ├── decisions │ │ │ ├── framework │ │ │ │ ├── framework-decision-authority.ts │ │ │ │ └── index.ts │ │ │ ├── gates │ │ │ │ ├── gate-enforcement-authority.ts │ │ │ │ ├── gate-enforcement-types.ts │ │ │ │ └── index.ts │ │ │ ├── index.ts │ │ │ ├── injection │ │ │ │ ├── constants.ts │ │ │ │ ├── index.ts │ │ │ │ ├── injection-decision-service.ts │ │ │ │ ├── internal │ │ │ │ │ ├── condition-evaluator.ts │ │ │ │ │ ├── hierarchy-resolver.ts │ │ │ │ │ └── index.ts │ │ │ │ ├── session-overrides.ts │ │ │ │ └── types.ts │ │ │ └── types.ts │ │ ├── index.ts │ │ ├── prompt-execution-pipeline.ts │ │ ├── stage.ts │ │ ├── stages │ │ │ ├── 00-dependency-injection-stage.ts │ │ │ ├── 00-execution-lifecycle-stage.ts │ │ │ ├── 00-request-normalization-stage.ts │ │ │ ├── 01-parsing-stage.ts │ │ │ ├── 02-inline-gate-stage.ts │ │ │ ├── 03-operator-validation-stage.ts │ │ │ ├── 04-planning-stage.ts │ │ │ ├── 05-gate-enhancement-stage.ts │ │ │ ├── 06-framework-stage.ts │ │ │ ├── 06a-judge-selection-stage.ts │ │ │ ├── 06b-prompt-guidance-stage.ts │ │ │ ├── 07-session-stage.ts │ │ │ ├── 07b-injection-control-stage.ts │ │ │ ├── 08-response-capture-stage.ts │ │ │ ├── 09-execution-stage.ts │ │ │ ├── 10-formatting-stage.ts │ │ │ ├── 10-gate-review-stage.ts │ │ │ ├── 11-call-to-action-stage.ts │ │ │ └── 12-post-formatting-cleanup-stage.ts │ │ └── state │ │ │ ├── accumulators │ │ │ ├── diagnostic-accumulator.ts │ │ │ ├── gate-accumulator.ts │ │ │ └── index.ts │ │ │ ├── index.ts │ │ │ └── types.ts │ ├── planning │ │ └── execution-planner.ts │ ├── types.ts │ └── validation │ │ ├── request-validator.ts │ │ └── schemas.ts ├── frameworks │ ├── framework-manager.ts │ ├── framework-state-manager.ts │ ├── framework-validator.ts │ ├── index.ts │ ├── integration │ │ ├── framework-semantic-integration.ts │ │ └── index.ts │ ├── methodology │ │ ├── framework-registry.ts │ │ ├── generic-methodology-guide.ts │ │ ├── index.ts │ │ ├── interfaces.ts │ │ ├── methodology-definition-types.ts │ │ ├── methodology-hot-reload.ts │ │ ├── methodology-schema.ts │ │ ├── registry.ts │ │ └── runtime-methodology-loader.ts │ ├── prompt-guidance │ │ ├── index.ts │ │ ├── methodology-tracker.ts │ │ ├── service.ts │ │ └── template-enhancer.ts │ ├── types │ │ ├── index.ts │ │ ├── methodology-types.ts │ │ └── prompt-guidance-types.ts │ └── utils │ │ ├── compliance-validator.ts │ │ ├── framework-detection.ts │ │ ├── index.ts │ │ ├── step-generator.ts │ │ └── template-enhancer.ts ├── gates │ ├── constants.ts │ ├── core │ │ ├── gate-definitions.ts │ │ ├── gate-loader.ts │ │ ├── gate-validator.ts │ │ ├── index.ts │ │ ├── llm-review-parser.ts │ │ ├── review-utils.ts │ │ ├── runtime-gate-loader.ts │ │ ├── temporary-gate-registry.ts │ │ └── types.ts │ ├── definitions │ │ ├── code-quality.json │ │ ├── content-structure.json │ │ ├── educational-clarity.json │ │ ├── framework-compliance.json │ │ ├── methodology-validation.json │ │ ├── research-quality.json │ │ ├── security-awareness.json │ │ └── technical-accuracy.json │ ├── gate-state-manager.ts │ ├── guidance │ │ ├── FrameworkGuidanceFilter.ts │ │ └── GateGuidanceRenderer.ts │ ├── index.ts │ ├── services │ │ ├── compositional-gate-service.ts │ │ ├── gate-reference-resolver.ts │ │ ├── gate-service-factory.ts │ │ ├── gate-service-interface.ts │ │ ├── index.ts │ │ └── semantic-gate-service.ts │ ├── templates │ │ ├── code_quality_validation.md │ │ ├── educational_clarity_validation.md │ │ ├── framework_compliance_validation.md │ │ ├── research_self_validation.md │ │ ├── security_validation.md │ │ ├── structure_validation.md │ │ └── technical_accuracy_validation.md │ ├── types.ts │ └── utils │ │ └── gate-definition-schema.ts ├── index.ts ├── logging │ └── index.ts ├── mcp-tools │ ├── config-utils.ts │ ├── constants.ts │ ├── index.ts │ ├── prompt-engine │ │ ├── core │ │ │ ├── chain-management.ts │ │ │ ├── index.ts │ │ │ ├── prompt-execution-service.ts │ │ │ └── types.ts │ │ ├── index.ts │ │ ├── processors │ │ │ └── response-formatter.ts │ │ └── utils │ │ │ ├── category-extractor.ts │ │ │ ├── classification.ts │ │ │ ├── context-builder.ts │ │ │ ├── guide.ts │ │ │ ├── tool-routing.ts │ │ │ └── validation.ts │ ├── prompt-manager │ │ ├── analysis │ │ │ ├── comparison-engine.ts │ │ │ ├── gate-analyzer.ts │ │ │ └── prompt-analyzer.ts │ │ ├── core │ │ │ ├── index.ts │ │ │ ├── manager.ts │ │ │ └── types.ts │ │ ├── index.ts │ │ ├── operations │ │ │ └── file-operations.ts │ │ ├── search │ │ │ ├── filter-parser.ts │ │ │ └── prompt-matcher.ts │ │ └── utils │ │ │ └── validation.ts │ ├── shared │ │ └── structured-response-builder.ts │ ├── system-control.ts │ ├── tool-description-manager.ts │ └── types │ │ └── shared-types.ts ├── metrics │ ├── analytics-service.ts │ ├── index.ts │ └── types.ts ├── performance │ ├── index.ts │ └── monitor.ts ├── prompts │ ├── category-maintenance.ts │ ├── category-manager.ts │ ├── converter.ts │ ├── file-observer.ts │ ├── hot-reload-manager.ts │ ├── index.ts │ ├── loader.ts │ ├── prompt-refresh-service.ts │ ├── prompt-writer.ts │ ├── promptUtils.ts │ ├── registry.ts │ └── types.ts ├── runtime │ ├── application.ts │ ├── context.ts │ ├── data-loader.ts │ ├── health.ts │ ├── methodology-hot-reload.ts │ ├── module-initializer.ts │ ├── options.ts │ ├── startup-server.ts │ └── startup.ts ├── semantic │ ├── configurable-semantic-analyzer.ts │ ├── integrations │ │ ├── index.ts │ │ └── llm-clients.ts │ ├── semantic-integration-types.ts │ └── types.ts ├── server │ ├── index.ts │ └── transport │ │ └── index.ts ├── smithery.yaml ├── text-references │ ├── argument-history-tracker.ts │ ├── conversation.ts │ ├── index.ts │ └── types.ts ├── tooling │ ├── action-metadata │ │ ├── README.md │ │ ├── definitions │ │ │ ├── index.ts │ │ │ ├── prompt-engine.ts │ │ │ ├── prompt-manager.ts │ │ │ ├── system-control.ts │ │ │ └── types.ts │ │ └── usage-tracker.ts │ └── contracts │ │ ├── _generated │ │ ├── mcp-schemas.ts │ │ ├── prompt_engine.generated.ts │ │ ├── prompt_engine.metadata.json │ │ ├── prompt_manager.generated.ts │ │ ├── prompt_manager.metadata.json │ │ ├── system_control.generated.ts │ │ ├── system_control.metadata.json │ │ └── tool-descriptions.json │ │ ├── adapter.ts │ │ ├── index.ts │ │ └── types.ts ├── types.ts ├── types │ ├── execution.ts │ └── index.ts └── utils │ ├── chainUtils.ts │ ├── constants.ts │ ├── errorHandling.ts │ ├── global-resource-tracker.ts │ ├── index.ts │ ├── jsonUtils.ts │ ├── resource-loader.ts │ ├── schema-validator.ts │ ├── service-manager.ts │ └── yaml │ ├── index.ts │ ├── yaml-file-loader.ts │ └── yaml-parser.ts ├── tests ├── helpers │ └── test-helpers.ts ├── setup.ts ├── tool-description-manager.test.ts └── unit │ ├── chain-session │ └── chain-session-manager.test.ts │ ├── execution │ ├── execution-context.test.ts │ ├── injection │ │ ├── condition-evaluator.test.ts │ │ ├── hierarchy-resolver.test.ts │ │ ├── injection-decision-service.test.ts │ │ └── session-overrides.test.ts │ ├── operators │ │ └── chain-operator-executor.test.ts │ ├── parsers │ │ ├── argument-parser.test.ts │ │ ├── argument-schema-validator.test.ts │ │ ├── command-parser.test.ts │ │ ├── symbolic-operator-parser.test.ts │ │ └── xml-encoding-workaround.test.ts │ ├── parsing-system.test.ts │ ├── pipeline │ │ ├── call-to-action-stage.test.ts │ │ ├── command-parsing-stage.test.ts │ │ ├── dependency-injection-stage.test.ts │ │ ├── execution-lifecycle-stage.test.ts │ │ ├── framework-stage.test.ts │ │ ├── gate-enhancement-stage.test.ts │ │ ├── gate-review-stage.test.ts │ │ ├── inline-gate-extraction-stage.test.ts │ │ ├── judge-selection-stage.test.ts │ │ ├── operator-validation-stage.test.ts │ │ ├── parsing-stage-commandtype.test.ts │ │ ├── pipeline-orchestrator.test.ts │ │ ├── planning-stage.test.ts │ │ ├── post-formatting-cleanup-stage.test.ts │ │ ├── prompt-guidance-stage.test.ts │ │ ├── request-normalization-stage.test.ts │ │ ├── response-capture-stage-verdict.test.ts │ │ ├── response-formatting-stage.test.ts │ │ ├── session-stage.test.ts │ │ ├── state │ │ │ ├── diagnostic-accumulator.test.ts │ │ │ ├── framework-decision-authority.test.ts │ │ │ ├── gate-accumulator.test.ts │ │ │ └── gate-enforcement-authority.test.ts │ │ ├── step-execution-stage.test.ts │ │ ├── step-response-capture-stage.test.ts │ │ └── symbolic-stage.test.ts │ ├── planning │ │ ├── execution-planner.test.ts │ │ └── execution-planner.test.ts (already done) │ └── validation │ │ └── command-type-discriminant.test.ts │ ├── frameworks │ ├── framework-validator.test.ts │ └── methodology │ │ └── yaml-methodology-loading.test.ts │ ├── gates │ ├── core │ │ ├── gate-loader.test.ts │ │ └── review-utils.test.ts │ ├── gate-review-session-continuity.test.ts │ ├── guidance │ │ ├── framework-guidance-filter.test.ts │ │ └── gate-guidance-renderer.test.ts │ └── services │ │ └── gate-services.test.ts │ ├── index-health.test.ts │ ├── mcp-tools │ ├── consolidated-tools.test.ts │ ├── prompt-engine │ │ ├── engine-validator.test.ts │ │ ├── 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