chore(deps-dev): bump ruff to 0.16.1 and prek to 0.4.12

[potiuk]

Summary

• Splits the non-breaking half out of chore(deps-dev): bump the python-deps group across 9 directories with 3 updates #1083. That PR grouped three updates; the
  mcp 1.28.1 → 2.0.0 bump in it is a breaking major that removes
  mcp.server.fastmcp and fails pytest (oauth-draft) with ModuleNotFoundError.
  That half is migrated separately in chore(deps): migrate gmail/oauth-draft to mcp 2.0 #1085.
• ruff 0.15.21/0.15.22 → 0.16.1 across all 30 workspace members; prek
  0.4.10 → 0.4.12 at the root. mcp deliberately left at 1.28.1.
• Excludes eval fixtures from ruff format. Ruff 0.16 began formatting Python
  inside Markdown fenced blocks — the reason chore(deps-dev): bump the python-deps group across 9 directories with 3 updates #1083 also failed ruff format for
  skill-evals. The ten files it wanted to rewrite are all
  evals/**/fixtures/**/report.md; not one is real source. Those files are test
  data: they simulate what a contributor actually pasted into an issue, single
  quotes and missing blank lines included, and several are prompt-injection cases
  whose whole point is that untrusted text reaches the model verbatim.
  Reformatting them would silently edit the input the eval grades against.

Type of change

• Skill change (.claude/skills/<name>/) — eval fixtures updated below
• Tool / bridge contract (tools/<system>/*.md)
• Python package (tools/*/ with pyproject.toml)
• Groovy reference impl
• Cross-cutting (RFC, AGENTS.md, sandbox, privacy-LLM)
• Documentation (docs/, README.md, CONTRIBUTING.md)
• Project template (projects/_template/)
• CI / dev loop (prek, workflows, validators)

Test plan

• prek run --all-files exits 0
• ruff format --check and ruff check pass for all 28 applicable members
• Full workspace pytest passes (run by the commit hook)
• Confirmed the diff touches only pyproject.toml files and uv.lock — no
  fixture file is modified by this PR

RFC-AI-0004 compliance

Not applicable — dependency-pin and lint-config change only; no skill or tool
behaviour, no new mutation, no new host access.

Linked issues

Refs #1083

Notes for reviewers

The interesting decision is the extend-exclude in tools/skill-evals/pyproject.toml
rather than accepting the reformat. Worth a look at the two representative diffs
ruff wanted to make:

--- evals/issue-reproducer/step-1-inventory/fixtures/case-4-injection-in-body/report.md
   from airflow.providers.sftp.hooks.sftp import SFTPHook
+
   hook = SFTPHook(ssh_conn_id="sftp_conn")

--- evals/pr-management-mentor/intervention/fixtures/case-2-missing-version/report.md
-     bash_task = BashOperator(task_id='test', bash_command='echo hello')
+     bash_task = BashOperator(task_id="test", bash_command="echo hello")

Both make the fixture less like what a real reporter writes, which is the
opposite of what a fixture is for.

Both this PR and the mcp migration touch uv.lock, so whichever merges second
needs a uv lock re-run. #1083 can be closed once both land.