Module Inventory

Machine-generated by scripts/sync_wiki.py. Do not hand-edit. Hand-written companion: Module Reference.

Package	Module	Purpose
`capstone_agent`	`__init__.py`	Local clinical data utilities used by the deterministic public demo.
`capstone_agent`	`a2a_server.py`	Expose this agent over the Agent2Agent (A2A) protocol (Day 5a).
`capstone_agent`	`agent.py`	Root agent definition — entry point for `adk run capstone_agent`.
`capstone_agent`	`app.py`	ADK `App` wrapper — the richer runtime around the root agent.
`capstone_agent`	`callbacks.py`	Security callbacks — defense in depth for agent safety.
`capstone_agent`	`catalog.py`	Dependency-light metadata for the public clinical agent topology.
`capstone_agent`	`clinical_schemas.py`	Clinical database schema definitions and query engine.
`capstone_agent`	`config.py`	Centralized configuration and secret management.
`capstone_agent`	`context.py`	Context engineering — token budgeting, compaction, structured assembly.
`capstone_agent`	`database.py`	SQLite database layer — real persistence for all clinical data.
`capstone_agent`	`document_processor.py`	Document processing — real PDF and image extraction using PyMuPDF and Gemini.
`capstone_agent`	`human_in_the_loop.py`	Human-in-the-loop / long-running operations (Day 2b).
`capstone_agent`	`llm.py`	Model registry and factory — the one place model selection happens.
`capstone_agent`	`memory.py`	Memory management — Layer 2 (Session State), Layer 3 (Long-Term), Layer 4 (A2A Context).
`capstone_agent`	`mock_data.py`	Deterministic mock data for the Clinical AI Command Center.
`capstone_agent`	`models.py`	Pydantic models for tool input/output contracts.
`capstone_agent`	`observability.py`	Observability — structured logging, tracing, and audit trail.
`capstone_agent`	`orchestration.py`	Multi-agent orchestration building blocks (Day 1b, 2a, 5a).
`capstone_agent`	`plugins.py`	Observability plugins (Day 4a).
`capstone_agent`	`prompts.py`	Clinical AI Command Center — agent instruction templates.
`capstone_agent`	`security.py`	Security module — PII detection, secret scanning, input sanitization.
`capstone_agent`	`tools.py`	Clinical AI Command Center — tool definitions (production).
`capstone_agent`	`vector_store.py`	Semantic vector store — Vertex AI embeddings over the clinical corpus.
`clinical_app`	`__init__.py`	Deterministic clinician product API.
`clinical_app`	`agent_runtime.py`	Deterministic product adapters for the real clinical agent tool layer.
`clinical_app`	`app.py`	FastAPI routes for clinician-facing deterministic application.
`clinical_app`	`document.py`	Document parsing and upload policy for clinical evidence files.
`clinical_app`	`live_bridge.py`	Lazy Google ADK execution bridge for live product mode.
`clinical_app`	`models.py`	Pydantic contracts for the clinician product API.
`clinical_app`	`repository.py`	Session-isolated mutable repository for deterministic product demos.
`clinical_app`	`system.py`	Real system introspection and tenant governance storage.
`clinical_app`	`tenancy.py`	Tenant registry for the clinician product — single source of truth.
`mcp_server`	`__init__.py`	(no docstring)
`mcp_server`	`server.py`	Clinical MCP server — real database-backed tools via Model Context Protocol.
`scripts`	`build_docs_site.py`	Build the standalone documentation hub served at /documentation.
`scripts`	`build_llm_wiki.py`	Script to compile the Obsidian Project Wiki into the Karpathy LLM Wiki structure.
`scripts`	`build_vector_index.py`	Backfill the semantic vector index for a tenant clinical database.
`scripts`	`check_harness.py`	Deterministically validate executable repository harness configuration.
`scripts`	`check_source_safety.py`	Repository safety gate for public source and commit metadata.
`scripts`	`export_diagrams.py`	Export Project Wiki draw.io diagrams into frontend public assets.
`scripts`	`generate_database_showcase.py`	Generate a large governed SQLite cohort for the database agent.
`scripts`	`generate_database_showcase_demo2.py`	Generate the second-platform database intelligence demo dataset.
`scripts`	`generate_extraction_showcase.py`	Generate production-like extraction packets for the extraction agent.
`scripts`	`generate_extraction_showcase_demo2.py`	Generate the second-platform extraction demo asset set.
`scripts`	`generate_live_test_data.py`	Generate a small live test dataset (database cohort, PDF, images) and run ETL ingestion.
`scripts`	`generate_multimodal_patient_showcase.py`	Generate multimodal patient bundles for the Q&A agent.
`scripts`	`generate_multimodal_patient_showcase_demo2.py`	Generate the second-platform multimodal Q&A demo bundle set.
`scripts`	`harness_runtime.py`	Lifecycle state and handoff runtime for the repository agent harness.
`scripts`	`ingest_capstone_live_samples.py`	Ingest the corrected multi-patient live sample dataset into the real Capstone tenant database.
`scripts`	`run_clinical_app_dev.py`	Run the clinical FastAPI app from the local Windows dev environment.
`scripts`	`showcase_clinical_core.py`	Shared clinically coherent synthetic cohort engine for all showcase generators.
`scripts`	`sync_harness.py`	Safely mirror the Claude harness into the cross-agent `.agents` tree.
`scripts`	`sync_wiki.py`	Deterministic Project Wiki and harness synchronization.
`tests`	`__init__.py`	(no docstring)
`tests`	`conftest.py`	Pytest configuration and shared fixtures for agent evaluation.
`tests`	`test_agent_eval.py`	Agent evaluation tests — validates agent behavior end-to-end.
`tests`	`test_callbacks.py`	Unit tests for the 3-layer security callbacks.
`tests`	`test_clinical_api.py`	Frontend contract tests for deterministic clinician product API.
`tests`	`test_clinical_tools.py`	Clinical tool integration tests — mock data consistency and HITL.
`tests`	`test_context.py`	Tests for context engineering utilities (Day 1 working memory).
`tests`	`test_document_parsing.py`	Document upload policy and extraction contract tests.
`tests`	`test_eval.py`	ADK evaluation harness test (Day 4b).
`tests`	`test_harness_runtime.py`	Tests for lifecycle state, handoff, and safe mirror harness tooling.
`tests`	`test_live_bridge.py`	Unit tests for the live-mode ADK bridge parsing helpers.
`tests`	`test_live_ingestion.py`	Unit tests for live mode ingestion, ETL, and database seeding.
`tests`	`test_memory.py`	Tests for memory governance (Day 3b).
`tests`	`test_orchestration.py`	Tests for the orchestration building blocks (Day 1b / 2a).
`tests`	`test_product_integration.py`	End-to-end contracts joining the clinical UI API to product state.
`tests`	`test_product_orchestration.py`	Contract tests for clinician-facing production workflow boundaries.
`tests`	`test_security.py`	Security test suite — validates all detection and sanitization functions.
`tests`	`test_showcase_generators.py`	Smoke tests for showcase data generators.
`tests`	`test_template_generators.py`	Unit tests for template-based showcase data generators.
`tests`	`test_tools.py`	Clinical tool validation tests — ensures consistent I/O contracts.
`tests`	`test_vector_store.py`	Unit tests for the semantic vector store (capstone_agent/vector_store.py).
`tests`	`test_versioned_api.py`	Unit tests for the versioned API backend endpoints (V1 and V2).
`tests`	`test_wiki_sync.py`	Unit tests for the deterministic wiki sync script (scripts/sync_wiki.py).