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