Dependency update sweep: bump all deps to latest and re-lock

[Copilot]

Description

Automated dependency sweep raising all versions across the uv workspace to their latest allowed releases, re-locking, and repairing the resulting toolchain fallout. Release-owned lines (graphrag-*== workspace pins, [project] version fields) and the intentionally-held graspologic-native>=1.2,<1.3 pin are left untouched.

Related Issues

Automated dependency update sweep.

Proposed Changes

• Version specifiers bumped in the root dev group and every packages/*/pyproject.toml. Notable: ruff 0.8→0.16, litellm 1.92.0→1.97.0, pydantic ~=2.10→~=2.13, typing-extensions ~=4.12→~=4.16, poethepoet 0.31→0.48, deptry 0.21→0.25, azure-cosmos ~=4.9→~=4.16, azure-storage-blob ~=12.24→~=12.30, azure-core ~=1.32→~=1.41, lancedb 0.34→0.37, json-repair 0.30→0.63, networkx 3.4→3.6, nltk 3.9→3.10, blis 1.0→1.3, textblob 0.18→0.20, tqdm 4.67→4.70, typer 0.16→0.27, mkdocs-material 9.5→9.7, coverage 7.6→7.15.
• uv.lock regenerated via uv lock --upgrade.
• ruff 0.16 fallout: ignore two new opinionated preview rules rather than churn the repo:
  • RUF105 (noqa-comments) — would rewrite 130+ existing # noqa comments to # ruff: ignore.
  • RUF201 (rule-codes-in-selectors) — would rewrite every rule code in the lint config to its long name.
  • ruff's docs explicitly note both are stylistic and safe to disable.
• ruff-format normalization of Python code blocks in 4 markdown/doc files under the newer formatter.
• Changelog: added a patch semversioner entry.

# pyproject.toml [tool.ruff.lint].ignore
# Opinionated preview rules (ruff >=0.16); we intentionally keep `# noqa`
# comments and rule codes in the lint selectors.
"RUF105",
"RUF201",

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

uv run poe check is green (ruff format, ruff lint, pyright) and uv run poe test_unit passes (317). Resolution/locking was performed against public PyPI because the Microsoft-internal index proxy is unreachable from the sandbox; it mirrors the same packages. A couple of tests require network-fetched data (NLTK wordnet, tiktoken encodings) unrelated to these bumps.

• Fixes Update Dependencies Sweep #2508