fix(agent): close the empty tool_calls 400 class at all three chokepoints (#83312, #77921)

[teknium1]

Fixes #83312. Fixes #77921. Closes #64335-class empty-tool_calls 400s on strict providers (DeepSeek v4, Moonshot/Kimi, Qwen/onerouter) at every layer that can create or forward the invalid shape.

The bug class

Strict OpenAI-compatible providers reject an assistant message carrying tool_calls: [] (or null) with a non-retryable HTTP 400 (Invalid 'messages[N].tool_calls': empty array). Because the poisoned message stays in the replayed in-memory history, every subsequent turn in the session fails the same way — the session is permanently wedged until the agent cache is cleared (#83312 observed this across 6 sessions; #77921 reproduced it three times in v0.19.1 despite the #59110 chokepoint fix).

The #58755/#59110 sanitizer strips tool_calls: [] where it sees it — but two later passes re-create the empty array after the strip has run, and some routes bypass the sanitizer entirely:

1. sanitize_api_messages tool_call_id dedup (runs after the empty-array drop): when every call on an assistant turn is a duplicate, kept_tcs collapses to [] and was written back as tool_calls: [] — re-creating the exact payload deleted a few passes earlier. This is the mechanism behind DeepSeek 400: assistant messages with empty tool_calls:[] wedge sessions permanently #83312's "sanitizer works in isolation but the array still reaches the wire", and it correlates with the Repaired N message-alternation violations log line because repair_message_sequence's consecutive-assistant merge is what produces the all-duplicates shape.
2. repair_message_sequence consecutive-assistant merge: the union branch preserved a stale tool_calls: [] on the surviving turn (and the repaired list is the live/persisted trajectory, so the [] was replayed every turn — Still reproducing in v0.19.1: empty tool_calls after repair_message_sequence (follow-up to #58755) #77921's finding that tool_calls = NULL rows become [] on load and survive the merge).
3. Transport boundary: auxiliary/custom-provider routes can reach ChatCompletionsTransport.convert_messages() without passing through sanitize_api_messages at all.

The fix (three chokepoints, salvaged from the three earliest PRs for each site)

• Dedup pass (agent/agent_runtime_helpers.py): when dedup removes ALL calls, drop the tool_calls key entirely instead of writing [] — salvaged from fix(sanitize): drop tool_calls key when dedup removes all calls #64345 by @liuhao1024 (earliest fix for this site, filed 2026-07-14).
• Repair merge (agent/agent_runtime_helpers.py): when neither merged turn carries calls, pop the stale tool_calls key at the source so the live/persisted trajectory is clean — salvaged from fix(session): drop empty tool_calls in repair_message_sequence (#77921) #77944 by @webtecnica (earliest fix for this site).
• Wire boundary (agent/transports/chat_completions.py): strip empty/null tool_calls on assistant messages in convert_messages(), the last transformation before the request — salvaged from fix(transport): strip empty/null tool_calls on assistant messages #72591 by @TurgutKural (earliest transport-boundary fix).

All three commits are cherry-picked with original authorship preserved.

Verification

tests/run_agent/test_message_sequence_repair.py            — 40 passed (incl. 3 new regressions)
tests/agent/transports/test_chat_completions_empty_tool_calls.py — new, passed
tests/agent/transports/test_chat_completions.py            — 46 passed (no regressions)
tests/run_agent/test_run_agent_codex_responses.py          — 47 passed (codex interim-turn exemption intact)

Duplicate/overlapping PRs covered by this class fix

#64345 (salvaged), #77944 (salvaged, was already closed into #78063), #72591 (salvaged), #83600, #83315, #86020, #77377 (agent_runtime_helpers portion), #64843, #82252 — all address subsets of the same class at one of these three sites.

Infographic

[webtecnica]

Thanks @teknium1 for consolidating the empty-tool_calls class into one fix and for salvaging our #77944 (repair-merge site) with authorship preserved — nice to see the three chokepoints (dedup, repair merge, wire boundary) covered from the earliest PRs for each. This closes the class properly!

[github-actions]

૮ >ﻌ< ა ci review

_{running on 8e73134 — fix(transport): scope empty tool_calls comment to transport-}

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⚠️ Warnings

OSV vulnerability scan · View job

5 known vulnerabilities found in pinned dependencies.

• CVE-2026-67213 in package-lock.json
• CVE-2026-67213 in website/package-lock.json
• CVE-2026-70608 in package-lock.json
• CVE-2026-56876 in package-lock.json
• CVE-2026-70606 in package-lock.json

How to fix:

Review the findings in the Security tab. Update the affected dependencies if a patched version is available.