fix: close operations dependency alerts

[abrichr]

What changed

• set explicit safe lower bounds for six affected direct and transitive Python dependencies
• refresh uv.lock to patched releases
• keep the floors in project metadata so later lock refreshes cannot select the affected versions

Why

The default branch has nine open Dependabot alerts across pymdown-extensions, urllib3, idna, requests, pytest, and Pygments. These packages support the public documentation build and operations scripts. The update closes the known affected version ranges without changing product behavior.

Validation

• Python 3.12: uv run pytest -q — 149 passed
• Python 3.10 isolated locked environment: 149 passed
• uv run python scripts/validate_docs.py
• uv run python scripts/check_published_version_claims.py --offline
• uv run mkdocs build --strict
• git diff --check