security: remediate additional issue 179 dependencies

[D3f0]

Summary

Follow-up security remediation for #179, based on the latest main.

Addresses

This PR refreshes the lockfile and upgrades compatible vulnerable dependencies:

• cryptography to 50.0.1
• docling to 2.127.0
• docling-core to 2.96.0
• GitPython to 3.1.62
• idna to 3.19
• langchain-core to 0.3.86
• langsmith to 0.12.5
• nltk to 3.10.3
• Pillow to 12.3.0
• protobuf to 6.33.6
• pyarrow to 25.0.1
• pyasn1 to 0.6.4
• pydantic-settings to 2.15.0
• PyJWT to 2.14.0
• python-multipart to 0.0.32
• setuptools to 84.0.0
• soupsieve to 2.9.2
• tornado to 6.5.10
• transformers to 4.57.6
• virtualenv to 21.7.10

Existing patched versions from the prior security PR remain in the lockfile, including LiteLLM, MCP, aiohttp, MkDocs Material, and pymdown-extensions.

Intentionally unresolved

• chromadb: issue 🔒 Security Alerts — IBM/Agentics #179 reports no patched version.
• json-repair: the current CrewAI constraint keeps version 0.25.2; remediation requires a CrewAI/dependency upgrade or upstream fix.
• torch: macOS x86_64 resolution remains pinned to 2.2.2 by the current Docling dependency graph; this requires a separate platform/dependency compatibility change.
• urllib3: current resolver constraints retain 2.3.0; further remediation requires upgrading the dependent packages that constrain it.

The exposed Google API key also requires external revocation and replacement and is not addressed by this code-only PR.

Verification

• uv lock --check: passed
• git diff --check: passed
• actionlint: passed
• Full pytest suite: 8 passed, 7 skipped
• Core package/security import smoke check: passed for the installed core environment

Release

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