Update dependencies to latest versions (dependency sweep)

[Copilot]

Description

Automated dependency sweep for the uv-workspace monorepo: regenerated uv.lock and bumped a few direct specifiers to their latest proxy-eligible versions.

Related Issues

Automated dependency sweep.

Proposed Changes

• Lockfile refresh — uv lock --upgrade picks up transitive/patch bumps (ruff, spacy, tiktoken, pydantic, protobuf, numpy 2.5.3 on py3.12+, etc.).
• Direct specifier bumps:
  • litellm==1.97.0 → 1.100.0 (graphrag-llm)
  • lancedb~=0.37.0 → ~=0.38.0 (graphrag-vectors)
  • coverage~=7.15 → ~=7.16 (root dev group)
• Held pins left intact:
  • numpy~=2.4 — 2.5+ drops Python 3.11 support (project is >=3.11).
  • graspologic-native<1.3 and nltk~=3.9.0 — golden-data holds.
• No graphrag-*== cross-package pins or version fields touched.

Checklist

• I have tested these changes locally.
• I have reviewed the code changes.
• I have updated the documentation (if necessary).
• I have added appropriate unit tests (if applicable).

Additional Notes

• poe check (ruff + pyright), test_unit (317), test_verbs (15), and all lancedb test_integration cases pass. The 4 integration failures are Azure blob/cache tests hitting a missing Azurite emulator (127.0.0.1:10000 connection refused) in the sandbox — unrelated to the bump.
• lancedb 0.38 emits deprecation warnings (table_names(), create_index() params); left unaddressed to keep the sweep minimal and avoid touching index behavior/golden data.

• Fixes Update Dependencies Sweep #2557

[Derek Worthen (dworthen)]

Copilot Need to bump semversion info with uv run semversioner add-change -t patch -d "<short description>".

[Copilot]

Copilot Need to bump semversion info with uv run semversioner add-change -t patch -d "<short description>".

Added a changelog entry via uv run semversioner add-change -t patch -d "Update dependencies to latest versions (dependency sweep)." in c60b08e.