What does this PR do?

The defensive branch in _build_assistant_message that was supposed to pin reasoning_content="" on DeepSeek thinking-mode tool-call turns never actually fired. It was gated on msg.get("tool_calls") — but tool_calls doesn't get added to msg until ~60 lines later in the same method, so the check was always falsy. Whenever DeepSeek returned reasoning_content=None on a tool-call turn (which happens intermittently in long sessions) and streaming captured no reasoning text, the message got persisted bare. The next replay 400'd:

Error from provider (DeepSeek): The reasoning_content in the thinking mode must be passed back to the API.

The same defect is reachable on Kimi/Moonshot thinking — same enforcement, no separate ticket but the shape's identical.

The fix replaces the dead elif with a single post-tool_calls pad that fires when:

• assistant_message.tool_calls is truthy (reading the SDK source of truth, not a not-yet-populated dict key, which is what caused the original bug); and
• reasoning_content isn't already set by an earlier branch (so we never clobber legitimate reasoning); and
• the active provider enforces echo-back.

Pulled the predicate into a new _needs_thinking_reasoning_pad() helper so _copy_reasoning_content_for_api shares it instead of re-inlining kimi or deepseek.

Related Issue

Fixes #17400

Type of Change

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

Changes Made

• run_agent.py: removed the dead pad branch in _build_assistant_message; added the unified post-tool_calls pad covering DeepSeek and Kimi/Moonshot; extracted _needs_thinking_reasoning_pad() and reused it in _copy_reasoning_content_for_api.
• tests/run_agent/test_deepseek_reasoning_content_echo.py: new TestBuildAssistantMessagePadsStrictProviders class — one parametrized test covering five provider/attribute combos (deepseek with reasoning_content=None, deepseek without the attribute at all, kimi-coding, custom-provider via api.moonshot.ai, plus an openrouter case to confirm we don't pad needlessly), and three standalone tests for "real reasoning preserved", "text-only turn untouched", "streamed reasoning wins over the empty pad". Folded the new helper's defaults into the existing _make_agent so the file doesn't end up with two parallel agent factories.

How to Test

1. pytest tests/run_agent/test_deepseek_reasoning_content_echo.py -q — 31 pass.
2. To confirm the new tests actually exercise the fix and not just pass trivially: git stash the change to run_agent.py, re-run the file, and 4 of the 8 new cases fail (the four that hit the previously-dead pad). Pop the stash; they pass again.
3. Wider sweep: pytest tests/run_agent/ -q — 1164 passed, 7 unrelated skips.

Checklist

Code

• I've read the Contributing Guide
• My commit messages follow Conventional Commits
• I searched for existing PRs to make sure this isn't a duplicate
• My PR contains only changes related to this fix (no unrelated commits)
• I've run the relevant test slice (tests/run_agent/) and all tests pass — 1164 passed, 7 unrelated skips. Skipped the full tests/ suite as the change is contained.
• I've added tests for my changes
• I've tested on my platform: macOS 15 (Darwin 25.4, arm64)

Documentation & Housekeeping

• Documentation updates — N/A (internal builder logic, no public surface change)
• cli-config.yaml.example — N/A
• CONTRIBUTING.md / AGENTS.md — N/A
• Cross-platform impact considered — pure Python message-builder logic, no platform-specific paths
• Tool descriptions/schemas — N/A