fix: address CodeRabbit Phase 7 review feedback

feat(phase7): implement Hypothesis Agent for mechanistic reasoning

fix: address CodeRabbit Phase 5 review feedback

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

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

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

feat(phase1): Foundation & Tooling complete

adds scaffolding