security: address remaining compatible issue 179 advisories

[D3f0]

Summary

Follow-up remediation for the remaining compatible dependency advisories in #179, based on merged main after PR #185.

Addresses

Refreshes the lockfile with current patched releases for:

• h2 → 4.4.1
• lxml → 6.1.3
• orjson → 3.12.0
• Pygments → 2.21.0
• python-dotenv → 1.2.3
• requests → 2.34.2

The merged baseline already includes patched versions of the other compatible advisories, including LiteLLM, MCP, aiohttp, cryptography, Docling, Docling Core, GitPython, idna, langchain-core, langsmith, nltk, Pillow, protobuf, pyarrow, pyasn1, pydantic-settings, PyJWT, python-multipart, setuptools, soupsieve, tornado, transformers, and virtualenv.

Remaining blockers

These alerts require coordinated major upgrades or upstream fixes and are intentionally not forced through incompatible constraints:

• chromadb: open critical/high alerts have no patched version reported.
• json-repair: requires CrewAI upgrade; current project constraints retain CrewAI 1.6.1.
• crewai-tools: patched release requires a newer CrewAI/Rich/MCP dependency set and conflicts with the current published constraints.
• transformers: patched releases require Transformers 5.x and a broader Docling/Hugging Face migration.
• langchain-core: patched 1.x conflicts with the current langchain-huggingface <0.4.0 constraint.
• torch: supported platform resolution still includes the Docling-pinned macOS x86_64 2.2.2 build; resolving this needs a platform support decision.
• urllib3: current dependency graph retains 2.3.0; upgrading to 2.7+ requires coordinated Kubernetes/dependent package updates.
• uv: the repository's installed tool is 0.9.17; updating the CI/bootstrap tool requires separate workflow/tooling review.
• Google API key: secret revocation and replacement must be completed externally.

Verification

• uv lock --check: passed
• git diff --check: passed
• actionlint: passed
• Core security import smoke test: passed
• Full pytest suite: 8 passed, 7 skipped

Release

After merging and externally rotating the Google API key, issue the security patch release through the normal release workflow.