fix(agent): strip orphan tool_calls in repair_message_sequence (#56980)

[hashbender]

What does this PR do?

Adds Pass 3 to repair_message_sequence that strips orphan tool_calls from assistant messages whose tool_call_ids have no matching tool result messages in the sequence. This prevents HTTP 400 "insufficient tool messages following tool_calls message" from strict providers (DeepSeek v4, Kimi) when context compaction, partial session resume, or retry loops leave dangling tool-call references.

Related Issue

Fixes NousResearch#56980

Type of Change

• 🐛 Bug fix (non-breaking change that fixes an issue)

Changes Made

• agent/agent_runtime_helpers.py: Added Pass 3 in repair_message_sequence — builds a set of all tool_call_ids present in tool messages, then strips tool_calls entries from assistant messages whose ids are absent. Keeps assistant text content intact; only removes the orphan calls.
• tests/run_agent/test_message_sequence_repair.py: Added 3 tests covering the new pass — orphan tool_calls at sequence end, parallel tool_calls with partial results missing, and no-op when all tool_calls have matching results.

How to Test

1. Run python -m pytest tests/run_agent/test_message_sequence_repair.py -v — all 28 tests should pass, including the 3 new ones (test_repair_strips_orphan_tool_calls_at_end, test_repair_strips_orphan_parallel_tool_calls, test_repair_preserves_complete_tool_calls).
2. The fix is verified by the new test test_repair_strips_orphan_tool_calls_at_end which simulates the exact scenario from the issue: an assistant message with tool_calls at the end of the sequence with no matching tool result.

Checklist

Code

• I've read the Contributing Guide
• My commit messages follow Conventional Commits (fix(scope):, feat(scope):, etc.)
• I searched for existing PRs to make sure this isn't a duplicate
• My PR contains only changes related to this fix/feature (no unrelated commits)
• I've run pytest tests/ -q and all tests pass
• I've added tests for my changes (required for bug fixes, strongly encouraged for features)
• I've tested on my platform: macOS 26.4.1

Documentation & Housekeeping

• I've updated relevant documentation (README, docs/, docstrings) — or N/A
• I've updated cli-config.yaml.example if I added/changed config keys — or N/A
• I've updated CONTRIBUTING.md or AGENTS.md if I changed architecture or workflows — or N/A
• I've considered cross-platform impact (Windows, macOS) per the compatibility guide — or N/A
• I've updated tool descriptions/schemas if I changed tool behavior — or N/A

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Mirror-of: NousResearch#56990
NousResearch#56990