feat: Phase 11 bioRxiv Preprint Integration (#19)

refactor: centralize embedding configuration in Settings

refactor: address final CodeRabbit feedback

fix(rag): address remaining CodeRabbit feedback

refactor: address CodeRabbit review feedback for Mario integration

fix(rag): use get_content() for BaseNode compatibility

fix(rag): apply lazy imports and use centralized config

feat: Integrate Mario's Modal code execution + LlamaIndex RAG

refactor: address CodeRabbit nitpicks for Phase 10

feat: Implement Phase 10 (ClinicalTrials.gov) with requests

feat: Complete Phase 9 Source Cleanup (Remove WebTool) (#14)

fix(report): add explicit JSON structure guidance in prompt

fix: address all CodeRabbit Phase 8 review feedback

fix: apply lazy init pattern and pydantic-ai fixes to ReportAgent (#12)

fix: address CodeRabbit Phase 7 nitpicks

fix: address CodeRabbit Phase 7 review feedback

feat(phase7): implement Hypothesis Agent for mechanistic reasoning

fix: address CodeRabbit Phase 6 review feedback

fix: address CodeRabbit Phase 5 review feedback

fix(phase6): critical fixes from senior audit

feat(phase6): Embeddings & Semantic Search implementation

fix(phase5): align configs and add agent tests

fix: linting and types for phase 5

fix: pass API keys explicitly to pydantic-ai providers

fix: pydantic-ai v1 compatibility and Anthropic model update

refactor(phase4): address CodeRabbit review

feat(phase4): Orchestrator and UI complete

fix: add type ignore comment for Agent instantiation in JudgeHandler

fix(tests): resolve mypy divergence and test failures

feat(phase3): implement judge slice (LLM Judge, Prompts, Models)

fix(phase2): address CodeRabbit review feedback + add examples

fix: resolve mypy divergence between make check and pre-commit

feat(phase2): implement search slice (PubMed, Web, Orchestrator) (#4)

feat(phase1): Foundation & Tooling complete

adds scaffolding

adds scaffolding