pyrefly: bump 0.42.0 → 0.61.0 and regenerate baseline

[rjpower]

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

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

🤖 Generated with Claude Code

[claude]

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Code review

🤖 No issues found. Checked for bugs and CLAUDE.md compliance.

The PR is a minimal, mechanical bump: a single literal version string in infra/pre-commit.py (0.42.0 → 0.61.0) plus a regenerated .pyrefly-baseline.json. No source code changes, no changes to [tool.pyrefly.errors], and the PR body states that pre-commit + pyrefly report ok with 0 live errors before and after.

Reviewers (2× CLAUDE.md/AGENTS.md compliance on Sonnet, 2× bug scan on Opus) each returned no issues. Style/quality rules do not apply to the auto-generated baseline JSON, and the new error categories surfaced by 0.61 (bad-dunder-all, bad-typed-dict-key, invalid-variance) are explicitly scoped to a later stage per the PR description.

• Check if PR should be reviewed
• Identify relevant CLAUDE.md / AGENTS.md files
• Summarize PR changes
• Run 4 parallel review agents
• Validate flagged issues
• Post review comment(s)
  • Branch: pyrefly/bump-0.61