Environment refresh + ty as pre-commit hook

[hmgaudecker]

Summary

Environment refresh plus migration of type checking from a pixi task to the
official ty-pre-commit hook, following the updated
ai-instructions
boilerplate.

ty: pixi task → pre-commit hook

• Add astral-sh/ty-pre-commit (v0.0.56) with --no-project so uv neither
  creates a .venv/uv.lock nor resolves deps; ty resolves third-party imports
  from [tool.ty] environment.python = ".pixi/envs/default".
• Drop the ty conda dependency and the ty pixi task.
• Skip the ty hook on pre-commit.ci (no pixi env, no network at hook
  runtime); the GitHub Actions run-ty job now runs
  pixi run prek run ty --all-files.
• Update AGENTS.md to describe the new flow.

Environment / tooling refresh

• Bump the .ai-instructions submodule to latest (d15d554 → 68dc3f4):
  modular tiers, distilled modules, ty-hook overhaul.
• pixi self-update to 0.72.0 and a full pixi update of pixi.lock
  (numpy 2.5, pandas 3.0.3, python 3.14.6, …).
• prek autoupdate: ruff v0.15.20, check-jsonschema 0.37.4,
  pyproject-fmt v2.25.1.
• Workflow version bumps (supersedes Bump the github-actions group across 1 directory with 3 updates #211): actions/checkout@v7,
  prefix-dev/setup-pixi@v0.10.0, pixi-version: v0.72.0,
  codecov/codecov-action@v7.
• .gitignore: add pytask.lock / pytask.lock.journal (newer pytask writes a
  root-level lock).

nodejs pinned to <26 (temporary)

The full pixi update pulled node 26, which breaks the run-docs job
(GET /favicon.ico 500 → ERR_STREAM_PREMATURE_CLOSE). Root cause is a known
Node regression (nodejs/node#63989):
a security backport added a data listener on idle http.Agent sockets, which
trips a latent node-fetch@2 keep-alive+gzip bug — and mystmd's book-theme
fetches the favicon over exactly that path. Same bug hit 24.17.0 (fixed 24.18.0)
and 22.23.0 (fixed 22.23.1); fix PR #64004
merged to main 2026-06-20 but is not yet in a released 26.x. node 25.9 is
unaffected only because it predates the backport — note it is EOL (2026-06-01),
so this pin should move to a fixed 26.x (and drop) once conda-forge ships one.

Superseded PRs

• Bump the github-actions group across 1 directory with 3 updates #211 (github-actions bumps) — folded into the workflow edits here.
• [pre-commit.ci] pre-commit autoupdate #205 (pre-commit.ci autoupdate) — folded into prek autoupdate +
  pyproject-fmt reordering.

Verification (local)

• prek run ty --all-files ✅ · full prek run --all-files ✅ (idempotent)
• All Python tests ✅ · paper PDF build ✅ · docs HTML build ✅ (node 25)
• task_compile_presentation (Slidev PDF export) needs a headless Chromium and
  is only exercised on CI.

🤖 Generated with Claude Code

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 99.34%. Comparing base (ae91725) to head (d6b8ec0).

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #213   +/-   ##
=======================================
  Coverage   99.34%   99.34%           
=======================================
  Files          10       10           
  Lines         153      153           
=======================================
  Hits          152      152           
  Misses          1        1           

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[hmgaudecker]

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