fix: restore bugfixes silently dropped by the v0.5.0 release commit

[atulya-singh]

I went looking for the cause of one reverted fix (#234, restored in #304) and found it wasn't a one-off. The v0.5.0 release commit reverted most of a month of merged PRs.

What happened

12d3fd8 ("release: AutoResearchClaw v0.5.0") is a single squashed commit — 318 files, +42,268/−8,632 — sitting directly on top of 84dad0a. Judging by what survived and what didn't, the v0.5.0 work was branched around 2026-04-09/10 and landed on 05-19, overwriting everything merged in between. Nothing in the commit mentions reverting anything.

The date cutoff is unusually clean:

merged	commit	fate
04-06	ad806b5 MiniMax preset URL / from-stage	intact
04-06	28478cc MCP path traversal, dispatcher failover	intact
04-07	5dc7fcc Responses API / MiniMax 404	intact
04-08	be89838 HITL collab fixes	intact
04-10	afccebe scripted HITL adapter	intact
04-10	e6a6dfa perf: lift regex compilation (#231)	reverted
04-10	7b57457 --from-stage without --output (#217)	fix kept, 212-line test file deleted
04-10	684ddb2 Gemini native adapter (#227)	file deleted
04-11	8ec230d retry error tracking (#234)	reverted (→ #304)
04-20	9f8d11d doctor gateway probe	reverted
04-20	61a92d8 Volcengine/BytePlus presets (#240)	reverted
04-20	28508f2 SOTA hallucination (#239 / fixes #238)	reverted
04-21	9f15247 search plan schema variants (#243)	reverted

Everything ≤04-08 survives; almost everything ≥04-10 is gone. 61a92d8 is the sharpest case — it came in via 84dad0a, the release commit's own parent, and was wiped by its own child.

I verified each of these against HEAD rather than trusting a diff heuristic — the refactor moved prompts.py into a prompts/ package, so "file gone" needed checking by hand. 5dc7fcc looked lost by line-matching but its content genuinely moved into prompts/ml.py; it's fine.

What this PR restores

Three correctness fixes whose removal is unambiguous, each mapping to an issue that's closed but reproducible again at HEAD:

Doctor gateway probe — health.py:177 was back to method="HEAD" on /models, byte-for-byte pre-fix. Gateways that reject HEAD but serve GET normally get reported as unreachable, which is what #292 and #241 were about.

SOTA hallucination (#238) — this one is the clearest evidence of an accident rather than a decision. The release didn't just drop the fix, it restored the exact prompt line the fix removed:

# researchclaw/prompts/ml.py:186 at HEAD — the line #239 deleted
"- State whether SOTA results exist on this benchmark and what they are.\n"
"- Add a 'Benchmark' subsection listing: name, source, metrics, "
"current SOTA (if known)."

The goal.md disclaimer is gone too. Notably prompts/ml.py:182 still has the anti-fabrication line from 5dc7fcc (04-07) while line 186 has the pre-#239 text (04-20) — the file is a snapshot from between those two dates, which is exactly the squash artifact you'd expect.

Search plan schema variants (#243) — _literature.py was back to plan.get("search_strategies", []), so a plan returned as search_phases / phases, or with dict-wrapped queries, silently produces zero queries.

What this PR deliberately does not restore

These may have been removed on purpose, and that's your call, not mine:

• Gemini native adapter (Gemini Native API Adapter #227) — llm/gemini_adapter.py is deleted and no gemini preset remains. Cleanly removed, no dangling imports, so this could well be intentional.
• Volcengine/BytePlus presets (LLM: add Volcengine and BytePlus presets #240) — gone from PROVIDER_PRESETS entirely (HEAD has: anthropic, deepseek, kimi-anthropic, minimax, novita, openai, openai-compatible, openrouter), and tests/test_volcano_provider.py was deleted.
• e6a6dfa (perf: lift repeated regex compilations to module level #231) — the regex hoisting is undone (_helpers.py:527 compiles per-call again). Perf only, and a separate concern.
• 7b57457 (fix: --from-stage without --output now finds existing run directory #217) — the fix survives, but its 212-line tests/test_from_stage_run_dir.py was deleted, so it's now unprotected.

Happy to send any of those as follow-ups if you confirm they weren't intentional.

Testing

pytest tests/ → 2799 passed, 56 skipped (2797 on main + the 2 tests added here).

#239's tests were dropped by the release too, so they're restored: the test_rc_prompts.py guard, and the test_rc_executor.py assertion that had to change because goal.md now leads with the disclaimer. I added a probe-method test for the doctor fix. I checked the new tests actually fail against un-restored source rather than passing vacuously:

FAILED tests/test_rc_health.py::test_check_llm_connectivity_probes_with_get_not_head
FAILED tests/test_rc_prompts.py::TestPromptManagerDefaults::test_topic_init_no_sota_hallucination

#243 has no test and I didn't add one. Its parsing sits inline in _execute_search_strategy, which needs run-dir artifacts, adapters and an LLM path to drive, so any test I wrote would be mostly mock scaffolding. Worth noting the original also shipped without tests — which is a large part of why it disappeared unnoticed for three months. If you want it covered, extracting the plan-parsing into a helper would make it a one-liner to test; happy to do that separately.

Worth considering

The single most useful change here isn't in the diff: whatever produced 12d3fd8 should rebase rather than squash onto main, or at minimum diff against main before landing. Five merged community PRs were reverted with no notice, and the only reason any of it surfaced is that I chased an unrelated 429 error message. I'd suggest a CI check that fails when a PR deletes a test file it didn't add — that alone would have caught #217, #240 and #227.

I'd also hold off closing #238, #241, #292 and #243 as fixed until this (or an equivalent) lands, since all four currently reproduce on main.