pyrefly: bump 0.42.0 → 0.61.0 and regenerate baseline (#4801)

## Summary

Bump `pyrefly` from `0.42.0` to `0.61.0` in `infra/pre-commit.py` and
regenerate `.pyrefly-baseline.json` so the new version's check passes
green. No code changes; no changes to `[tool.pyrefly.errors]`.

**Baseline deltas** (see `logs/pyrefly-tightening/stage1-bump-diff.md`
for detail):

- Baseline JSON: **2080 → 2031 lines** (-49); suppressed errors **173 →
169**.
- **85** old suppressions disappeared (fixed upstream or check retuned).
- **66** new suppressions appeared (new checks / regressions).
- **51** stable across the bump.
- Live (non-suppressed) errors: **0 → 0**. Pre-commit pyrefly: **ok**.

**Notable category shifts:**

- `bad-specialization` **1 → 68** — big expansion; almost all are
`Self@...` vs `DataclassInstance` bound on `dataclasses.replace(self,
...)` in levanter LM head models. Likely an upstream stub regression;
Stage 3 will decide fix-vs-suppress.
- `inconsistent-overload` **30 → 10** (-20), concentrated in
`haliax/nn/scan.py` and `haliax/_src/scan.py` — upstream overload
resolution improved.
- `redundant-cast` **15 → 0** — check retired/retuned.
- `invalid-param-spec` **2 → 0** — retired.
- `bad-return` **33 → 20**, `bad-override` **32 → 21**, `bad-assignment`
**13 → 4**, `unsupported-operation` **15 → 6** — broad upstream
improvements.

**New categories surfaced by 0.61** (not suppressed — they live in the
baseline and get triaged in Stage 2/3):

- `bad-dunder-all` (4) — names in `__all__` not defined in module
(`lib/fray/v1/cluster/__init__.py`, etc.). Real bugs.
- `bad-typed-dict-key` (3) — invalid TypedDict key access in
`lib/marin/src/marin/cluster/config.py`. Real bugs.
- `invalid-variance` (2) — TypeVar variance issues.

## Test plan

- [x] `./infra/pre-commit.py --all-files` passes on a clean worktree of
this branch (Pyrefly reports `ok`).
- [x] `uvx pyrefly@0.61.0 check --baseline .pyrefly-baseline.json`
reports 0 errors (suppressions only).
- [x] `[tool.pyrefly.errors]` in `pyproject.toml` is untouched (Stage 1
scope).
- [ ] CI green on PR.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Author: rjpower