Dependency update sweep

[Copilot]

Description

Automated dependency sweep: re-locked the uv workspace and raised version specifiers to their latest eligible releases across the root dev group and every packages/*/pyproject.toml, repairing the resulting toolchain fallout.

Related Issues

Automated dependency update sweep.

Proposed Changes

• Specifier bumps: floors raised to newly-locked versions across all workspace members; notable: lancedb 0.34→0.37 (cap was blocking newer releases), ruff 0.8→0.16, pydantic→2.13, numpy→2.4, pyarrow→25.0.1, json-repair→0.63, typer→0.27, poethepoet→0.48.
• Lockfile: regenerated via uv lock --upgrade / uv sync --all-packages (Microsoft feed proxy only).
• ruff 0.16 preview fallout: ignore RUF105 (noqa-comments) and RUF201 (rule-codes-in-selectors) in [tool.ruff.lint] rather than rewriting every # noqa; applied the formatter's new Markdown code-block formatting to 4 doc/README files.
• nltk held on ~=3.9.0: 3.10 changes POS-tagger/tokenizer output, shifting deterministic noun-phrase counts and breaking test_extract_graph_nlp golden data — held with an explanatory comment (mirrors the graspologic-native hold), pending a deliberate golden-data refresh.
• Untouched (release-owned / deliberate holds): graphrag-*== cross-package pins, [project] version fields, graspologic-native>=1.2,<1.3, litellm==1.92.0.
• Added a semversioner patch changelog entry.

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 clean; test_unit (317) and test_verbs (15) pass. The 4 test_integration failures are environmental — they target the Azurite emulator at 127.0.0.1:10000, which isn't running in the sandbox.
• lancedb 0.37 emits a create_index() deprecation warning (metric/num_partitions API); functional but worth a follow-up migration to the IvfPq config API.

• Fixes Update Dependencies Sweep #2515