fix(agent): append system_prompt to the Claude Code preset instead of replacing

[Mihaiii]

Why append instead of replace

ClaudeAgentOptions.system_prompt accepts either a plain string or the claude_code preset dict. A plain string replaces Claude Code's entire default system prompt — the only way to keep the default is {"type": "preset", "preset": "claude_code", "append": ...}. coder_eval passes the experiment's system_prompt straight through as a string, so any experiment that sets even a one-line prompt silently strips every behavioral instruction the harness ships with.

That is exactly what the skills-repo experiments do. The nightly config sets an innocuous sandbox guard:

https://github.com/UiPath/skills/blob/main/tests/experiments/nightly.yaml#L39-L40

system_prompt: |
  You are a coding agent. Do not access files in sibling runs/* directories. Everywhere else is permitted.

(same pattern in tests/experiments/default.yaml#L21, smoke.yaml#L39, smoke-windows.yaml#L23, and the skill-comparison templates)

One sentence of sandbox policy costs the whole Claude Code system prompt.

Observed impact (skills nightly, skill-rpa-execution-map-greenfield)

The task is a turn-budget gate (max_turns: 10, expected 6) that assumes the agent batches tool calls per turn. Every claude-sonnet-5 run exhausted the cap; pass/fail depended on where the cap happened to land. Transcript analysis across four runs (31172161551, 31174117722 ×3 attempts, 31178128981, 31179344004 ×2 attempts):

1. Zero parallel tool calls, ever. Example distribution (run 31179344004, attempt 2): 30 assistant messages — 0 multi-tool, 19 single-tool, 11 with no tool call at all. The instruction to emit independent tool calls together in one message lives in the default system prompt; with it gone, Sonnet paid one turn per call and blew the 10-turn budget in 7/7 attempts. Skill-doc prose telling the agent to batch (added and strengthened twice in UiPath/skills) was read in-transcript and changed nothing — a reference file cannot substitute for the missing system-level contract.
2. Narration bloat. 10–11 assistant messages per run contained no tool call, just interim commentary — the default prompt's conciseness/minimal-output rules were gone.
3. Tool-choice drift. Runs used Bash cat/sed/find where the default prompt directs the dedicated Read/Grep/Glob tools (e.g. cd TextReport && cat project.json && cat Main.xaml), losing the harness's file-tracking and permission integration.

Beyond the observed items, replacing the prompt also drops the default guidance on code-reference formatting, task management, professional tone, and the security guardrails — none of which an experiment author intends to disable when adding a sandbox-scoping sentence.

The change

• claude_code_agent.py: when system_prompt is configured, wrap it as SystemPromptPreset(type="preset", preset="claude_code", append=...) so the default prompt survives and the experiment text is appended. None still means the untouched SDK default.
• agent_config.py: system_prompt field description updated ("appended to the agent's default system prompt" — previously "Replaces").
• tests/test_agent.py: two tests via the existing _capture_sdk_options pattern (append wrapping; None passthrough).

Behavioral note for existing consumers

Every experiment that sets system_prompt switches from replace to append semantics with this release. For the known consumers (sandbox-scoping one-liners) this is the intended repair. An experiment that deliberately relied on full replacement to suppress default Claude Code behavior would need a different mechanism.

Judge (agent_judge.py) and user-simulator paths construct their own options and are unaffected.

🤖 Generated with Claude Code

[github-actions]

Claude finished @Mihaiii's task in 1m 46s —— View job

---

🔍 Reviewing PR #92: Fix system_prompt append behavior

Working on review...

Todo List:

• Read .github/code_review.md for review guidelines
• Read CLAUDE.md for project conventions
• Review the full diff (git diff origin/main...HEAD)
• Read each changed file in full context
• Perform cross-file consistency checks
• Check "what's missing" analysis
• Post comprehensive review feedback

[akshaylive]

Review: fix(agent): append system_prompt to the Claude Code preset instead of replacing

PR #92 by @Mihaiii · fix/sys-prompt-append → main · OPEN · reviewed against f066834

The diagnosis here is right and worth fixing: passing a plain string to ClaudeAgentOptions.system_prompt does replace Claude Code's default prompt, which silently strips the behavioral guidance (parallel tool batching, conciseness, tool-use conventions) that tasks are implicitly written against — so any task setting system_prompt has been measuring a crippled agent. The SystemPromptPreset fix is the correct mechanism, it's minimal and proportionate, and it comes with tests. Two things block merge, though. First, _build_options has a second consumer the PR wasn't scoped for: agent_judge sets config.system_prompt to its grading persona, so the judge now runs with the coding-agent preset prepended — that can move scores for byte-identical agent output. Second, the system_prompt is None branch is left as-is, and the SDK maps None to --system-prompt "", meaning the far more common no-system_prompt case still loses the preset — half the bug survives, and one of the new tests asserts that state is correct. Overall 8.9 / 10, weakest axis Evaluation Harness Quality at 5.5 / 10.

Summary

Axis	Score	🔴	🟠	🟡	🔵	Top Issue
1. Code Quality & Style	9.9 / 10	0	0	0	1	Last sentence of the new comment restates the code
2. Type Safety	9.9 / 10	0	0	0	1	SystemPromptPreset imported from a non-root SDK module with no rationale note
3. Test Health	8.3 / 10	0	1	1	2	test_system_prompt_none_leaves_sdk_default pins a false contract
4. Security	9.9 / 10	0	0	0	1	Forced append widens the agent_judge trust boundary
5. Architecture & Design	9.0 / 10	0	1	0	0	One shared base field now has three contradictory per-agent semantics
6. Error Handling & Resilience	10.0 / 10	0	0	0	0	No findings
7. API Surface & Maintainability	9.0 / 10	0	1	0	0	docs/agents/CLAUDE_CODE.md:102 now contradicts the code
8. Evaluation Harness Quality	5.5 / 10	1	1	1	0	agent_judge's grading prompt is now appended to the coding-agent preset

Overall Score: 8.9 / 10 · Weakest Axis: Evaluation Harness Quality at 5.5 / 10
Totals: 🔴 1 · 🟠 4 · 🟡 2 · 🔵 5 across 8 axes reviewed.

Blockers

1. The change reconfigures the scoring instrument, not just the agent under test. criteria/agent_judge.py:265 does config.system_prompt = _SYSTEM_PROMPT on a ClaudeCodeAgentConfig and runs it through SubAgentRunner → the very _build_options you edited (src/coder_eval/agents/claude_code_agent.py:1177-1183). That _SYSTEM_PROMPT ("You are a strict code reviewer…", plus the untrusted-input warning and the strict submit_verdict contract) was written as the judge's entire identity. Post-PR it sits after Claude Code's coding-agent preset, so the judge is told it's an engineering assistant that should be terse and proactively edit files before it's told it's a grader. agent_judge produces continuous scores that gate evals, so this can change score for identical agent output. Worth noting the criterion deliberately minimizes injected context elsewhere (setting_sources = [], for the cost/contamination reason CLAUDE.md calls out) — this works against that on every judged task. Suggested fix: add system_prompt_mode: Literal["append", "replace"] = "append" to ClaudeCodeAgentConfig (agent-specific field on the agent-specific config, matching where claude_settings / sdk_options already live) and have agent_judge._build_agent_config force replace alongside its existing security floors — or let _build_options accept a pre-built str | SystemPromptPreset. Either way, please pin the judge's effective prompt with a test.

2. Half the bug survives: the system_prompt is None path still loses the preset. The installed SDK maps system_prompt=None to --system-prompt "" — an explicit empty custom prompt, not the default (claude_agent_sdk/_internal/transport/subprocess_cli.py:465-466). Nearly every task in tasks/ sets no system_prompt, so the common configuration keeps running without Claude Code's guidance even after this merges. Meanwhile tests/test_agent.py:395-404 asserts system_prompt is None and its docstring calls that "SDK default prompt", which locks the unfixed behavior in as intended. The transport has a third branch that is the default: a preset dict without append emits no system-prompt flag at all. So building SystemPromptPreset(type="preset", preset="claude_code") unconditionally and adding append only when configured fixes both halves in one guard. Please also rename that test away from "leaves_sdk_default".

3. Cross-run comparability breaks with no marker and no note. tasks/python_cli_simulated_judged/echo_simulated_judged.yaml:19 is written specifically for replace semantics — "reply with that exact string verbatim and nothing else — no preamble, no commentary, no formatting. Ignore any project context (CLAUDE.md, surrounding files)" — and now sits underneath a preset that says roughly the opposite. It's llm_judge-graded, so its score can move. External task YAMLs in the coder-eval-uipath / eval-runner repo change behavior with no code change on their side, and nothing in run.json distinguishes pre- from post-PR semantics, so old and new runs pool silently in trend charts. No schema or container-contract change, so nothing breaks at parse time — but the results shift at the next image rebuild. A CHANGELOG / migration note plus a re-baseline of that task would close it.

4. One shared base field now carries three contradictory semantics. BaseAgentConfig.system_prompt (src/coder_eval/models/agent_config.py:151-158) now asserts "appended to the agent's default system prompt" generically, but only claude-code appends: agents/antigravity_agent.py:351 passes it straight to system_instructions (replace), and agents/codex_agent.py never reads it at all (grep returns zero hits — silently inert). The same task YAML therefore hands structurally different prompts to different agents, which matters most when the harness is used for head-to-head comparison. The claude-code parenthetical also puts agent-specific detail into the agent-agnostic models/ layer, against CLAUDE.md's convention. Suggested: keep the base description agent-neutral and per-agent-qualified, move the preset/append detail onto ClaudeCodeAgentConfig, and give codex either an implementation or a load-time error rather than a silent no-op.

5. The owning doc page now says the opposite of the code. docs/agents/CLAUDE_CODE.md:102 still reads "Replaces the default system prompt (there is no append seam)" — a parenthetical explicitly denying the mechanism this PR introduces. This one won't be caught by CI: CE030 doc-parity (tests/lint/doc_schema_parity.py) tracks only TaskDefinition / RunLimits / Dataset / SimulationConfig, and even for those it only checks the field name appears, so a semantics inversion passes silently. Please update the row in this PR.

Non-blocking, but please consider before merge

Tests

• tests/test_agent.py:380-393 asserts only the in-process dict shape. Since SystemPromptPreset is a bare TypedDict, the constructor is dict(...) with no validation, so the assertion compares a literal against a dict the line under test just built — it pins the values (useful) but nothing about the SDK contract. Feeding the captured options into SubprocessCLITransport(prompt="x", options=captured_options[0])._build_command() and asserting --append-system-prompt present / --system-prompt absent is ~4 lines, runs offline, and is the only assertion that survives an SDK shape change. Worth noting nothing in the suite today (including test_agent_golden_master.py and test_claude_settings_enforcement_live.py) would have caught the original bug either.

Reproducibility

• exclude_dynamic_sections is left unset, so the preset's dynamic sections (working directory, git status, auto-memory) are injected — in a tempdir sandbox that puts a run-varying path in the system prompt. Setting exclude_dynamic_sections=True keeps the prompt static and cache-friendly; the SDK re-injects the stripped content into the first user message, so nothing is lost. Also worth a doc line that the prompt baseline is now CLI-version-dependent, cross-referencing environment_info.claude_code_cli (already captured in run.json via utils.py:467-474, which is a nice mitigation).

Docs

• docs/agents/ANTIGRAVITY.md and docs/agents/CODEX.md don't document system_prompt at all, so after this change there's no page stating the per-agent semantics. Worth adding a row to each while updating CLAUDE_CODE.md.

Nits

• src/coder_eval/agents/claude_code_agent.py:1177-1183 — the comment's first two lines carry real "why" (the SDK footgun); the third ("Always keep the default via the SDK preset and append the configured prompt after it") is a prose transcription of the line below it. Consider dropping it.
• src/coder_eval/agents/claude_code_agent.py:30 — SystemPromptPreset isn't in claude_agent_sdk's root __all__, so claude_agent_sdk.types is the only route (correct, and evaluation/verdict_tool.py:21 sets precedent). A one-line note saying so would match the treatment the _internal.transport import three lines above already gets.
• tests/test_agent.py:380-404 — no case for system_prompt: "". It currently yields append="" (harmless), but nothing pins it, so a future refactor to if self.config.system_prompt: would silently route empty-string configs into the preset-loss path with the suite still green. Note antigravity_agent.py:351 uses or None and treats "" as unset, so the two agents already disagree here.
• No test pins the per-agent divergence (codex ignoring the field, antigravity replacing), nor that system_prompt_file reaches the same append path — the two halves are covered separately but never joined.
• CodeQL's py/unused-import at claude_code_agent.py:31 is a stale pre-existing note, not something this PR introduced — the new symbol is used both as an annotation and as a runtime constructor call, and ruff F401 is clean.

What's Missing

Parallel paths

• 🔴 criteria/agent_judge.py / evaluation/sub_agent.py are the second consumer of _build_options and weren't considered — triggered by claude_code_agent.py:1177-1183.
• 🟠 agents/codex_agent.py and agents/antigravity_agent.py weren't touched, so the shared field they inherit now diverges from its own description — triggered by models/agent_config.py:151-158.

Tests

• 🔴 Nothing pins agent_judge's effective ClaudeAgentOptions.system_prompt, so the judge's persona change is invisible.
• 🟡 No transport-level assertion — the surface the original bug lived on is untested.
• 🔵 No case for system_prompt: ""; no test pinning the per-agent divergence.

Downstream consumers

• 🟠 External task YAMLs in coder-eval-uipath / eval-runner that set system_prompt change behavior with no change on their side; run.json records nothing marking which semantics were used.
• 🟠 tasks/python_cli_simulated_judged/echo_simulated_judged.yaml needs re-baselining or rewording.

Display & mapping dicts

• Nothing identified — no enum, FinalStatus, or union value changed, so no reports*.py mapping needs extending.

Harness & Lint Improvements

Static checks (lint / type)

• Extend CE030 (tests/lint/doc_schema_parity.py) to BaseAgentConfig and the per-agent config subclasses, mapped to their docs/agents/*.md pages — would have caught the CLAUDE_CODE.md:102 drift at make lint time (name-level only; a semantics inversion still needs a human).
• New CEnnn: a Field(description=...) on a shared base model in models/agent_config.py must not contain a registered agent-kind string — grep-shaped, would have caught the claude-code parenthetical leaking into the agnostic base model, and permanently enforces the agent-agnostic-core convention.
• New CEnnn (CE031-style dead-config extension): every concrete agent module must reference each behavior-driving BaseAgentConfig field by name, or carry an EXEMPT entry — would have surfaced that codex_agent.py reads system_prompt nowhere.
• Not statically reachable: the judge-persona and comparability findings need semantic knowledge of what the CLI does with a flag and what a prompt means to a model. Those stay tests and review.

Harness improvements

• A transport-level parity test over the system_prompt matrix (None / "" / set / preset-without-append) asserting exact argv — needs the installed SDK's arg construction, so it can't be static; would have caught both test-health findings and the original bug.
• Record the resolved system-prompt mode (or a hash of the effective prompt) in the run record — needs runtime state; makes the silent pre/post pooling visible.
• A pinning test for agent_judge's effective ClaudeAgentOptions — needs a live options capture.

Top 5 Priority Actions

1. Stop the judge from inheriting the coding-agent preset. Add a replace seam on ClaudeCodeAgentConfig (or let _build_options accept a pre-built str | SystemPromptPreset) and have agent_judge._build_agent_config force replace, next to its existing setting_sources=[] and ignore_patterns floors. Pin it with a test. This is the only finding that can move scores for identical agent output.
2. Fix the other half of the bug: the system_prompt is None path. Emit SystemPromptPreset(type="preset", preset="claude_code") unconditionally and add append only when configured, so the unset case produces no system-prompt flag (the CLI default) instead of --system-prompt "". Then rewrite and rename test_system_prompt_none_leaves_sdk_default — today it asserts something the SDK does not do.
3. Add a transport-level assertion feeding the captured options into SubprocessCLITransport._build_command() and checking --append-system-prompt is present and --system-prompt absent. Four lines, offline, and the only test that survives an SDK shape change.
4. Update docs/agents/CLAUDE_CODE.md:102 (currently the exact opposite of the new behavior) and reword BaseAgentConfig.system_prompt's description to state the per-agent semantics honestly rather than asserting append generically. Add the field to ANTIGRAVITY.md / CODEX.md while there.
5. State the blast radius and re-baseline. Add a CHANGELOG / migration note that system_prompt semantics changed from replace to append, re-check echo_simulated_judged at HEAD, and flag it for the external coder-eval-uipath pipeline owners.

---

Change class: complex — it changes prompt-construction semantics on a shared config field, and that field feeds the agent_judge scoring path, so correctness requires reasoning about consumers outside the diff.
Stats: 1 🔴 · 4 🟠 · 2 🟡 · 5 🔵 across 8 axes reviewed.

[Mihaiii]

@akshaylive The review is addressed now, please have a second look. Antigravity doesn't need any change because it already is on append mode by default, not replace.

[uipreliga]

Review: fix(agent): append system_prompt to the Claude Code preset instead of replacing

PR #92 by @Mihaiii · fix/sys-prompt-append → main · OPEN · reviewed against 3083fc8

Change class: complex — changes the system-prompt regime for every Claude Code run (preset-append instead of replace) and adds a new system_prompt_mode public config field plus a cross-agent environment_info marker; correctness requires reasoning about SDK prompt semantics and score comparability across the boundary.

The codebase is in strong shape — clean security, error handling, and test hygiene, with no critical findings and every issue traceable to one new feature — but the system_prompt_mode: replace rollout is incomplete in ways that silently change behavior: the user simulator's persona now ships behind the Claude Code coding-agent preset (altering every dialog-mode evaluation), a replace request with no prompt is silently ignored while run.json still labels the run "replace", and the persisted preset dict leaks into the report's System Prompt row; fix those three plus the Antigravity empty-string divergence and the stale append-only prose, and this lands comfortably at its 9.6.

Summary

Axis	Score	🔴	🟠	🟡	🔵	Top Issue
1. Code Quality & Style	9.9 / 10	0	0	0	1	Empty-string system_prompt resolves to three different regimes across the three agents, all reported as append
2. Type Safety	8.9 / 10	0	0	2	1	system_prompt_mode="replace" with no system_prompt silently runs the preset/append regime while environment_info.system_prompt_semantics records "replace" (no validator, no test)
3. Test Health	9.8 / 10	0	0	0	2	system_prompt_semantics marker tests are tautological — no test asserts the marker reaches run.json or reflects real append behavior
4. Security	10 / 10	0	0	0	0	—
5. Architecture & Design	9 / 10	0	1	0	0	system_prompt_mode="replace" hardening is applied only at the agent_judge callsite — no SubAgentRunner-level guard and UserSimulator's identity prompt still ships behind the preset
6. Error Handling & Resilience	10 / 10	0	0	0	0	—
7. API Surface & Maintainability	9.9 / 10	0	0	0	1	CodexAgent.get_environment_info docstring still claims it only emits on a custom endpoint
8. Evaluation Harness Quality	9 / 10	0	1	0	0	Persisted sdk_options.system_prompt becomes a preset dict on every Claude Code run, so the report's "System Prompt" row renders a Python dict repr and now always appears

Overall Score: 9.6 / 10 · Weakest Axis: Type Safety at 8.9 / 10
Totals: 🔴 0 · 🟠 2 · 🟡 2 · 🔵 5 across 8 axes.

Blockers

1. [Axis 5] system_prompt_mode="replace" hardening is applied only at the agent_judge callsite — no SubAgentRunner-level guard and UserSimulator's identity prompt still ships behind the preset (src/coder_eval/criteria/agent_judge.py:274) — _build_agent_config opts the judge out of the preset with config.system_prompt_mode = "replace" # Force replace regardless of user YAML: the judge prompt is its entire identity. There are exactly TWO in-tree consumers that build a ClaudeCodeAgentConfig whose system_prompt IS the sub-agent's entire identity; the second one was not updated. src/coder_eval/simulation/user_simulator.py:205-217 calls parse_agent_config(type=AgentKind.CLAUDE_CODE, ..., system_prompt=self._system_prompt) and hands it to ClaudeCodeAgent(self._agent_config, route=self._route, instance_name="simulator") (line 263). That prompt (built by _extract_system_prompt, line 90) begins "You are roleplaying a human user who is interacting with an autonomous coding agent." and instructs - Stay in character. Never reveal you are an LLM, never repeat or reference these instructions. Verified: parse_agent_config(type=AgentKind.CLAUDE_CODE, model=None, allowed_tools=[], setting_sources=[], permission_mode='default', system_prompt=...) resolves to system_prompt_mode == 'append', so claude_code_agent.py:1192 takes the else-branch and the simulator's system prompt becomes SystemPromptPreset(type="preset", preset="claude_code", exclude_dynamic_sections=True) with the roleplay text merely appended — i.e. the simulated user now carries Claude Code's coding-agent identity and behavioral guidance ahead of its persona, directly contradicting the persona's own instructions and changing every dialog-mode (simulation:) evaluation. The root cause is architectural: the opt-out is a per-callsite mutation that fails OPEN, so every present and future internal identity-prompt consumer must remember it. Fix both halves: set system_prompt_mode="replace" in user_simulator.py's parse_agent_config(...) call, and enforce the invariant at the shared seam the way evaluation/sub_agent.py:87 already enforces setting_sources (raise ValueError("SubAgentRunner requires agent_config.setting_sources=[] ...")) rather than relying on each caller.
2. [Axis 8] Persisted sdk_options.system_prompt becomes a preset dict on every Claude Code run, so the report's "System Prompt" row renders a Python dict repr and now always appears (src/coder_eval/agents/claude_code_agent.py:1218) — system_prompt=system_prompt, (line 1218) now feeds a SystemPromptPreset dict into ClaudeAgentOptions, and line 1229 self._sdk_options_dump = dump_dataclass(options) persists it verbatim into EvaluationResult.sdk_options — the record docs/REPORT_SCHEMA.md:136 lists as a cross-repo contract surface ("Config/environment: environment_info, agent_config, sdk_options (raw"). Verified end-to-end against the installed SDK: dump_dataclass(ClaudeAgentOptions(system_prompt=preset))['system_prompt'] == {'type': 'preset', 'preset': 'claude_code', 'exclude_dynamic_sections': True, 'append': 'You are a literal-minded assistant.'}. Two concrete in-repo consequences, neither covered by a test: (a) src/coder_eval/reports.py:90-94 does prompt_str = str(settings_source["system_prompt"]).replace("\n", " "), so the Markdown and HTML "System Prompt" row now renders the Python dict repr instead of the prompt text; (b) that row previously vanished when no prompt was configured (system_prompt is None) and now ALWAYS appears, showing {'type': 'preset', 'preset': 'claude_code', 'exclude_dynamic_sections': True}. The existing guard tests/test_reports.py:904 (assert "**System Prompt**" not in report_md) still passes only because its fixture hardcodes "system_prompt": None (tests/test_reports.py:883) — a value a real Claude run can no longer produce. Fix: unwrap for reporting/persistence (store the effective prompt string plus the mode) or teach collect_agent_settings_rows the preset shape, add a report test fed from a real dump_dataclass(options) rather than a hand-built dict, and state the sdk_options.system_prompt type change in docs/REPORT_SCHEMA.md so the external coder-eval-uipath / eval-runner consumer can be updated in lockstep.

Non-blocking, but please consider before merge

1. [Axis 2] system_prompt_mode="replace" with no system_prompt silently runs the preset/append regime while environment_info.system_prompt_semantics records "replace" (no validator, no test) (src/coder_eval/agents/claude_code_agent.py:1251) — The regime is decided by a two-term condition at claude_code_agent.py:1192 — if self.config.system_prompt_mode == "replace" and self.config.system_prompt is not None: — but the telemetry marker at claude_code_agent.py:1251 reports only one term: return {"system_prompt_semantics": self.config.system_prompt_mode}. Nothing validates the pair. Verified empirically at PR HEAD (parse_agent_config(type=AgentKind.CLAUDE_CODE, system_prompt_mode='replace') then ClaudeCodeAgent._build_claude_query(...)): system_prompt sent: {'type': 'preset', 'preset': 'claude_code', 'exclude_dynamic_sections': True} while env_info: {'system_prompt_semantics': 'replace'}. So an operator running -D agent.system_prompt_mode=replace without a prompt gets the FULL claude_code coding-agent preset — the opposite of what agent_config.py:206 documents ("'replace' sends it as the ENTIRE system prompt") and of docs/agents/CLAUDE_CODE.md's new row ("replace sends system_prompt as the entire system prompt (no preset)") — and run.json labels that run "replace", so the marker whose own docstring says "trend dashboards must not pool scores across that boundary" (claude_code_agent.py:1249) mis-buckets it. Fix both halves: (a) add a @model_validator(mode="after") on ClaudeCodeAgentConfig (mirroring check_prompt_exclusivity at agent_config.py:188) rejecting system_prompt_mode == "replace" when system_prompt is None — the inverse guard of the new conditional; (b) derive the marker from the same expression the options builder uses (extract an _effective_prompt_mode() -> Literal["append", "replace"] helper called from both line 1192 and line 1251) so the run record can never disagree with the wire. Add a test for the replace + unset pair — the five new tests in tests/test_agent.py cover append / unset / empty-string / replace-with-prompt but not this combination.
2. [Axis 2] Documentation asserts system_prompt is "never a replacement"/"always kept", contradicted by the system_prompt_mode: replace added in the same PR (src/coder_eval/models/agent_config.py:154) — agent_config.py:154 now reads "Custom system prompt, appended to the agent's default system prompt — never a replacement. " on BaseAgentConfig — the vendor-neutral base every agent kind inherits. Fifty lines below, agent_config.py:201-208 adds system_prompt_mode: Literal["append", "replace"] whose own description says "'replace' sends it as the ENTIRE system prompt.", and src/coder_eval/criteria/agent_judge.py:272 forces exactly that (config.system_prompt_mode = "replace"). The absolute "never" is therefore false for the flagship agent on its most security-relevant path. It is also false for NoneAgentConfig (agent_config.py:308): grep -n "system_prompt" src/coder_eval/agents/noop_agent.py returns nothing — the NoOp agent neither appends nor replaces, it drops the field — and the same holds for any out-of-tree BYOA BaseAgentConfig subclass, since system_prompt_mode lives only on ClaudeCodeAgentConfig. Per CLAUDE.md ("Field descriptions ... defined once in Pydantic models" / "Single Source of Truth"), this description is the schema SSOT surfaced in -D did-you-mean help and generated docs. Soften it to the honest contract, e.g. "Custom system prompt. Built-in agents layer it on top of their default prompt rather than replacing it; Claude Code can opt out via system_prompt_mode: replace. Each agent's doc page (docs/agents/) states the exact mechanism." — keeping the per-agent doc pointer already on line 155.

Nits

1. [Axis 1] Empty-string system_prompt resolves to three different regimes across the three agents, all reported as append (src/coder_eval/agents/codex_agent.py:1290) — The new Codex plumbing at line 1290-1291 uses if self.config.system_prompt is not None: / options["developer_instructions"] = self.config.system_prompt, matching Claude Code's is not None at claude_code_agent.py:1196 — and the PR even pins that semantics with test_system_prompt_empty_string_appends_empty ("a future truthiness refactor must not route it into the preset-loss path"). But src/coder_eval/agents/antigravity_agent.py:351 still reads system_instructions=self.config.system_prompt or None, so system_prompt: "" is silently dropped there while it is forwarded on the other two. Technique 2 (parallel code paths): the PR deliberately unifies system-prompt semantics across agents yet leaves this one divergence, and the new empty-string test covers only Claude Code. Either switch Antigravity to if self.config.system_prompt is not None for parity, or document why or None is required by the Antigravity SDK.
2. [Axis 2] New test helper _transport_command(options) has an untyped parameter, and the union-typed system_prompt is indexed unchecked (tests/test_agent.py:380) — tests/test_agent.py:380 declares def _transport_command(options) -> list[str]: — the return is typed but the parameter is bare, so the helper accepts anything and options.cli_path = "claude" (line 389) / SubprocessCLITransport(prompt="x", options=options) (line 390) are unchecked. Annotate it options: ClaudeAgentOptions. Relatedly, tests/test_agent.py:441 does assert captured_options[0].system_prompt["append"] == "" — ClaudeAgentOptions.system_prompt is str | SystemPromptPreset | SystemPromptFile | None (claude_agent_sdk/types.py:1752), so subscripting it is only silent because the pre-existing _capture_sdk_options at tests/test_agent.py:184 is annotated -> "list" (unparameterized) and pyright excludes tests/ anyway. Parameterize that helper as -> list[ClaudeAgentOptions] and assert the whole dict (as the sibling tests at lines 400-405 already do) instead of indexing the union, so an SDK reshape of SystemPromptPreset surfaces as a typed failure rather than a runtime TypeError.
3. [Axis 3] system_prompt_semantics marker tests are tautological — no test asserts the marker reaches run.json or reflects real append behavior (tests/test_agent.py:461) — test_environment_info_reports_system_prompt_semantics (tests/test_agent.py:461) asserts only default_agent.get_environment_info() == {"system_prompt_semantics": "append"} on the agent method; the same is true of the Codex (tests/test_codex_agent.py:334) and Antigravity (tests/test_antigravity_agent.py:67) markers. Nothing exercises the merge seam self.result.environment_info.update(self.agent.get_environment_info()) at src/coder_eval/orchestrator.py:1217 with a non-empty agent dict: tests/test_route_seam_exhaustiveness.py:90 passes agent=None (fake = SimpleNamespace(route=r, eval_route=r, result=SimpleNamespace(environment_info={}), agent=None)), and the two _setup tests use DummyAgents whose get_environment_info is return {} (tests/test_orchestrator.py:606 and :670). Since environment_info in run.json is the cross-repo contract consumed by the external eval-runner, add one assertion that an agent-supplied key survives the merge into EvaluationResult.environment_info.
4. [Axis 3] _transport_command helper overclaims: exclude_dynamic_sections never reaches argv, so the reproducibility half of the change is untested (tests/test_agent.py:380) — The helper's docstring says it "pins the SDK contract (which flag the transport emits)", and the tests assert on --append-system-prompt / --system-prompt presence. But exclude_dynamic_sections is not a CLI flag: claude_agent_sdk/_internal/client.py:148-155 extracts it from the preset dict and _internal/query.py:209-210 sends it as request["excludeDynamicSections"] in the control-protocol initialize message (if self._exclude_dynamic_sections is not None: request["excludeDynamicSections"] = self._exclude_dynamic_sections). The SDK comment there notes "older CLIs ignore unknown initialize fields". So the only coverage of the unconditional exclude_dynamic_sections=True (src/coder_eval/agents/claude_code_agent.py:1195) is the dict-literal assertion; the run-comparability claim documented in docs/agents/CLAUDE_CODE.md is unverified. Either narrow the _transport_command docstring to say it pins argv only, or add an assertion that the SDK's extraction path picks the flag up from the options we build.
5. [Axis 7] CodexAgent.get_environment_info docstring still claims it only emits on a custom endpoint (src/coder_eval/agents/codex_agent.py:940) — Line 940 still reads Only emits when a custom endpoint is configured (CODEX_BASE_URL). On a — but the PR made line 951 seed info: dict[str, Any] = {"system_prompt_semantics": "append"} and line 954 return it unconditionally, which the amended test at tests/test_codex_agent.py:339 pins (assert agent.get_environment_info() == {"system_prompt_semantics": "append"}). Reword the docstring so the conditional applies to the routing keys (codex_base_url_host / codex_wire_api / codex_api_version), not the whole dict; the new inline comment at 947-950 documents the unconditional key but the docstring above it was left stale.

What's Missing

Parallel paths:

• 🟠 criteria/agent_judge.py forces system_prompt_mode="replace" for the judge, but the other in-tree consumer whose system_prompt is a sub-agent's entire identity — simulation/user_simulator.py:205-214 → ClaudeCodeAgent(..., instance_name="simulator") at line 263 — was not updated, so the simulated user now runs the claude_code coding-agent preset with its roleplay persona merely appended (verified: options.system_prompt == the preset dict + append). Set system_prompt_mode="replace" there and enforce the invariant at the shared SubAgentRunner seam (evaluation/sub_agent.py:85, which already hard-fails on setting_sources) rather than per callsite. (trigger: src/coder_eval/criteria/agent_judge.py) (restates: Axis 5: system_prompt_mode="replace" hardening applied only at the agent_judge callsite)
• 🔵 The PR unified system_prompt is not None handling in claude_code_agent.py:1196 and codex_agent.py:1290 (and pinned it with test_system_prompt_empty_string_appends_empty), but left antigravity_agent.py:351 on system_instructions=self.config.system_prompt or None — system_prompt: "" is still silently dropped on that one agent while all three report system_prompt_semantics: append. (trigger: src/coder_eval/agents/antigravity_agent.py) (restates: Axis 1: Empty-string system_prompt resolves to three different regimes across the three agents)
• 🔵 The new system_prompt_semantics marker was hand-copied into three agents but not defaulted on the ABC: agent.py:325-337 still returns {} and its docstring only mentions "routing/environment details", and agents/noop_agent.py (plus any out-of-tree BYOA / plugin agent, e.g. the coder_eval_uipath Delegate agent) emits no marker at all. A consumer therefore cannot distinguish "pre-marker run" from "agent that never emits it" — declare the key on Agent.get_environment_info's contract (or supply the append default on the base) so new agents inherit it. (trigger: src/coder_eval/agents/antigravity_agent.py)
• 🔵 docs/AB_EXPERIMENTS.md:136-138 enumerates the agent-dict keys an experiment variant may override (system_prompt / system_prompt_file, setting_sources, claude_settings, sdk_options) and was not extended with the new system_prompt_mode — the field most likely to be A/B-tested (append vs replace arms) is missing from the one page that lists variant levers. (trigger: src/coder_eval/models/agent_config.py)

Tests:

• 🟡 The five new tests cover append-with-prompt, unset, empty-string, replace-with-prompt and the marker, but not the fourth cell of the 2×2: system_prompt_mode="replace" with system_prompt unset — the combination that silently falls through to the preset while environment_info records "replace". Add that case alongside the validator that should reject it (allowing system_prompt_file, which task_loader inlines later). (trigger: tests/test_agent.py) (restates: Axis 2: system_prompt_mode="replace" with no system_prompt silently runs the preset/append regime)
• 🟡 No test feeds a real dump_dataclass(options) into reports.collect_agent_settings_rows, so the new preset-dict shape reaching the Markdown/HTML "System Prompt" row is uncovered; the existing guard tests/test_reports.py:904 still passes only because its fixture hardcodes "system_prompt": None (line 884) — a value a real Claude Code run can no longer produce. (trigger: tests/test_agent.py) (restates: Axis 8: Persisted sdk_options.system_prompt becomes a preset dict on every Claude Code run)
• 🟡 The PR newly documents Antigravity's append mechanism (system_prompt → system_instructions → TemplatedSystemInstructions) and adds an env-marker test, but grep -rn "system_instructions" tests/ returns zero hits — nothing anywhere pins that system_prompt actually reaches the Antigravity SDK, so both the documented claim and the or None drop are untested. Add a _build-level assertion mirroring the new Codex developer_instructions tests. (trigger: docs/agents/ANTIGRAVITY.md)
• 🟡 tests/test_user_simulator.py asserts only the rendered prompt string (sim.system_prompt), never the SDK options the simulator agent is built with — which is exactly why the preset now silently wrapping the simulator persona passes CI. Add a simulation-side assertion on the resolved ClaudeAgentOptions.system_prompt (or on _agent_config.system_prompt_mode), the same shape as the new judge test in tests/test_agent_judge_criterion.py. (trigger: src/coder_eval/agents/claude_code_agent.py) (restates: Axis 5: system_prompt_mode="replace" hardening applied only at the agent_judge callsite)
• 🔵 All three new marker tests assert the agent method's hardcoded return value; nothing exercises orchestrator.py:1217 (environment_info.update(self.agent.get_environment_info())) with a non-empty agent dict (the orchestrator DummyAgents return {} and test_route_seam_exhaustiveness.py:90 passes agent=None), so no test proves the marker actually lands in run.json. (trigger: tests/test_agent.py) (restates: Axis 3: system_prompt_semantics marker tests are tautological)

Downstream consumers:

• 🟡 The marker's stated purpose — "trend dashboards must not pool scores across that boundary" (claude_code_agent.py:1249) — has no consumer: grep -rn "system_prompt_semantics" evalboard returns nothing, evalboard/lib/runs.ts:415 types environment_info as an opaque Record, and every stored historical run lacks the key entirely. Either add the evalboard segmentation/back-fill rule (absent key ⇒ pre-append regime) or soften the docstring to "recorded for offline segmentation". (trigger: src/coder_eval/agents/claude_code_agent.py)
• 🟡 docs/REPORT_SCHEMA.md — the documented cross-repo run-record contract consumed by coder-eval-uipath / eval-runner — was not touched: neither the new environment_info.system_prompt_semantics key (line 52) nor the type change of sdk_options.system_prompt from str | null to a preset dict (line 136) is stated, so external consumers that string-handle that field get no notice. (trigger: src/coder_eval/agents/claude_code_agent.py) (restates: Axis 8: Persisted sdk_options.system_prompt becomes a preset dict on every Claude Code run)
• 🔵 Cumulative-budget caps are computed from token counts that just changed: with the preset now always sent (main sent --system-prompt ""), every turn's input/cache-creation tokens rise by the full claude_code prompt, so run_limits.max_input_tokens / max_total_tokens / max_usd values calibrated pre-change (e.g. tasks/smoke_budget_exceeded.yaml, tasks/smoke_cost_budget_exceeded.yaml, experiments/default.yaml) and any commands_efficiency budgets may now trip or pass differently. Nothing in the PR revisits those thresholds. (trigger: src/coder_eval/agents/claude_code_agent.py)

Display & mapping dicts:

• 🟡 reports.collect_agent_settings_rows (reports.py:90-94) was not extended for the new value shape: its str(settings_source["system_prompt"]) now renders a Python dict repr in both Markdown and HTML, the row that used to disappear when no prompt was set is now always present, and ~72 of the 200 SYSTEM_PROMPT_PREVIEW_CHARS are consumed by preset metadata before any prompt text. (trigger: src/coder_eval/agents/claude_code_agent.py) (restates: Axis 8: Persisted sdk_options.system_prompt becomes a preset dict on every Claude Code run)
• 🔵 The new system_prompt_mode field is not rendered anywhere in the report surfaces — collect_agent_settings_rows has no row for it in either the agent_config or sdk_options table — so a report reader can only infer the regime from the raw Environment key/value dump. Add a "System Prompt Mode" row next to "System Prompt" when it is non-default. (trigger: src/coder_eval/models/agent_config.py)

Daily/nightly:

• 🟠 Blast radius on the production/nightly path is unstated outside a docs blockquote: on main an unset system_prompt produced --system-prompt "" (SDK subprocess_cli.py:465-466 — an explicitly EMPTY prompt), so every Claude Code task in every suite now runs with the full claude_code preset instead. Pass rates, turn counts, token/cost baselines and stored trend series all shift at this commit; the PR should say whether nightly baselines are re-run, from which run_id the series is re-based, and how historical runs (which carry no system_prompt_semantics key) are labelled. (trigger: src/coder_eval/agents/claude_code_agent.py)
• 🟡 The exclude_dynamic_sections=True reproducibility guarantee is unverified on the containerized (production) path: it is not a CLI flag but a control-protocol excludeDynamicSections initialize field (SDK _internal/query.py:209-210), which the SDK's own comment notes older CLIs silently ignore, while docker/Dockerfile pins CLAUDE_CODE_VERSION=2.1.177 and docker/Dockerfile.runtime mirrors it. Nothing asserts a minimum CLI version or states what the docker-driver nightly actually gets. (trigger: src/coder_eval/agents/claude_code_agent.py)
• 🟡 The Codex half is a silent behavior change on any existing Codex task or experiment variant that sets agent.system_prompt: the field was previously DROPPED and is now injected as developer_instructions (codex_agent.py:1291). The new environment_info comment records the boundary, but the PR does not state which Codex-backed suites are affected or whether their scores need re-baselining alongside the Claude Code ones. (trigger: src/coder_eval/agents/codex_agent.py)

Harness & Lint Improvements

Static checks (lint / type):

• [ce-lint] New rule CE032 NoTruthyOptionalConfigCoercion (tests/lint/rules/ce032_no_truthy_optional_config_coercion.py, added to ALL_RULES in tests/lint/runner.py, tested in tests/test_custom_lint.py). Pattern forbidden: truthiness collapse of an agent-config field inside src/coder_eval/agents/** — any BoolOp(Or) whose left operand is an attribute chain rooted at self.config (self.config.system_prompt or None), and any bare if self.config.<field>: / if not self.config.<field>: where the field is declared str | None / list | None on a BaseAgentConfig subclass. Required form is the explicit is None / is not None test that claude_code_agent.py:1196 and codex_agent.py:1290 already use. Scope the AST match to self.config.* roots only, so the legitimate env-var idioms (os.getenv("GEMINI_API_KEY") or None, codex_agent.py:1065) stay legal — a grep of src/ shows self.config.<x> or None occurs exactly once today, at agents/antigravity_agent.py:351, i.e. the rule lands with one violation and no cleanup tail. Prevents: Finding 1 (system_prompt: "" silently dropped by antigravity_agent.py:351's self.config.system_prompt or None while Claude Code and Codex forward it) — and permanently pins the empty-string semantics that test_system_prompt_empty_string_appends_empty only asserts for one of the three agents.
• [ce-lint] New rule CE033 EnvInfoMarkersDerivedNotRestated (tests/lint/rules/ce033_env_info_markers_derived.py, wired into tests/lint/runner.py). Pattern forbidden: inside a get_environment_info method body, returning a raw config attribute as a telemetry value (return {"system_prompt_semantics": self.config.system_prompt_mode}, claude_code_agent.py:1251) when that same self.config.<field> also appears as an operand of a multi-term BoolOp test elsewhere in the same module (claude_code_agent.py:1192: system_prompt_mode == "replace" and system_prompt is not None). The fix the rule forces is the one the finding recommends: extract _effective_prompt_mode() -> Literal["append", "replace"] and call it from both the options builder and the marker, so the persisted run record cannot disagree with the wire. Generalizes cleanly: any run-record marker whose value is decided by more conditions than the marker reads is a mis-bucketing bug for trend dashboards. Prevents: Finding 2 (system_prompt_mode="replace" with no system_prompt runs the preset/append regime on the wire while environment_info.system_prompt_semantics — persisted to run.json via orchestrator.py:1217 — records "replace").
• [ce-lint] New rule CE034 InternalIdentityPromptModeExplicit (tests/lint/rules/ce034_identity_prompt_mode_explicit.py, wired into tests/lint/runner.py). Pattern forbidden: anywhere in src/coder_eval/** outside models/agent_config.py, a call to parse_agent_config(...) that passes system_prompt= (or an assignment <cfg>.system_prompt = ...) without system_prompt_mode being set in the same function body. Today that yields exactly two callsites: criteria/agent_judge.py:274 (compliant — sets system_prompt_mode = "replace" two lines below) and simulation/user_simulator.py:205-214 (violating — the roleplay persona silently ships behind the claude_code coding-agent preset). Same anti-fail-open shape as the existing SubAgentRunner setting_sources=[] guard at evaluation/sub_agent.py:85-89, but a lint rule rather than a runtime check because UserSimulator instantiates ClaudeCodeAgent directly (user_simulator.py:263) and never passes through SubAgentRunner, so no shared runtime seam can see it. Prevents: Finding 6 / high (the simulated user's identity prompt is appended to Claude Code's coding-agent preset, changing every simulation: dialog-mode evaluation) — and stops the next internal identity-prompt consumer from inheriting the same fail-open default.
• [ce-lint] New rule CE035 InheritedFieldDescriptionMentionsModifier — a doc-surface/whole-tree check next to tests/lint/doc_schema_parity.py (CE030) and wired as a dedicated @pytest.mark.lint class in tests/test_custom_lint.py, not as a BaseRule (it reasons over the whole model tree, per the CE026-CE031 precedent). Two mechanical assertions over src/coder_eval/models/agent_config.py: (a) if a subclass adds a field whose name is <inherited_field>_<suffix> (system_prompt_mode modifying the base's system_prompt), the inherited field's Field(description=...) must mention the modifier field name inline; (b) a base-model field description must not contain an absolute negation (never a replacement, always kept) about behavior a subclass field can invert. agent_config.py:154 ("appended ... — never a replacement") violates both, given system_prompt_mode: Literal["append", "replace"] 47 lines below on ClaudeCodeAgentConfig and criteria/agent_judge.py:274 forcing replace. This is the CLAUDE.md "field descriptions defined once in Pydantic models / Single Source of Truth" principle made mechanical. Prevents: Finding 3 (base BaseAgentConfig.system_prompt description contradicts the system_prompt_mode: replace added in the same PR, and is also wrong for NoneAgentConfig and out-of-tree BYOA subclasses), plus the parallel stale prose row at docs/agents/CLAUDE_CODE.md:102.
• [ruff] Enable ANN (flake8-annotations) in [tool.ruff.lint] select in pyproject.toml — select = ["E", "F", "I", "N", "W", "UP", "B", "SIM", "RUF", "ANN", "PLR0915", "PLR0912"] — with [tool.ruff.lint.per-file-ignores] "tests/**" = ["ANN201", "ANN202"] so test functions themselves stay unannotated while ANN001 (missing parameter annotation) still applies to test helpers. tests/ currently has zero type enforcement (pyright excludes it, ruff selects no ANN), which is why a new helper shipped with a bare parameter. Prevents: Finding 4 (def _transport_command(options) -> list[str]: at tests/test_agent.py:380 — return typed, parameter bare, so options.cli_path = ... and SubprocessCLITransport(options=options) are unchecked). Expect a one-time annotation sweep over existing fixture helpers; that sweep is the point.
• [pyright] Add a tests-scoped second pyright pass: a pyrightconfig.tests.json with "include": ["tests"], "typeCheckingMode": "basic", and the three settings that matter here promoted to error — reportMissingTypeArgument, reportOptionalSubscript, reportIndexIssue — then wire it into make typecheck as a second invocation (pyright && pyright -p pyrightconfig.tests.json). The main [tool.pyright] block deliberately excludes tests, so nothing today type-checks the test suite at all; a separate config keeps src/ at standard while letting tests/ start at a permissive basic baseline. Prevents: Finding 4's second half: the unparameterized -> "list" on _capture_sdk_options (tests/test_agent.py:184) that makes captured_options[0] an Unknown, and the unchecked subscript of a union at tests/test_agent.py:441 (ClaudeAgentOptions.system_prompt is str | SystemPromptPreset | SystemPromptFile | None) — so an SDK reshape of SystemPromptPreset surfaces as a typed failure in make verify instead of a runtime TypeError.

Harness improvements (not statically reachable):

• Prompt-regime matrix test in tests/test_agent.py: parametrize the full cartesian product of (system_prompt_mode ∈ {unset, append, replace}) × (system_prompt ∈ {unset, "", "text"}) × (system_prompt_file ∈ {unset, set}), and for each cell assert three things agree: the ClaudeAgentOptions.system_prompt value actually built by _build_claude_query, the transport argv (--system-prompt vs --append-system-prompt vs neither), and get_environment_info()["system_prompt_semantics"]. The PR's five new tests cover append / unset / empty-string / replace-with-prompt but not replace-with-unset-prompt — the one broken cell. Pair it with the corrected validator (system_prompt_mode == "replace" requires system_prompt is not None or system_prompt_file is not None, since task_loader.py:230-241 inlines the file later). Why not static: CE033 can force the marker and the wire to share one expression, but only a runtime build of the SDK options can prove which regime each (mode, prompt) pair actually lands in — the fallback value is produced by constructing SystemPromptPreset and handing it to the vendored SDK, not by any statically-comparable source expression. Prevents: Finding 2 (silent replace → preset fallback with a mislabelled run.json marker).
• Agent-parity conformance suite driven by AgentRegistry: one parametrized test that enumerates every registered agent kind (so a new agent inherits the assertions automatically, the CE025 registry-enumeration pattern applied to tests) and asserts the shared prompt contract per agent — system_prompt=None omits the vendor field, system_prompt="" is forwarded (not dropped), system_prompt="x" reaches the vendor field, and get_environment_info() carries system_prompt_semantics. Today each of the three agents has its own bespoke, differently-shaped assertion (tests/test_agent.py:466, tests/test_codex_agent.py:339, tests/test_antigravity_agent.py:72) and only Claude Code has the empty-string case. Why not static: CE032 catches the specific or None spelling, but semantics divergence can also arrive as if not prompt: return or a vendor SDK that itself drops empty strings — proving equivalence needs the config actually driven through each agent's options builder. Prevents: Findings 1 and 5 (per-agent empty-string divergence; three hand-written, mutually inconsistent marker tests).
• environment_info propagation test at the orchestrator seam: assert that a DummyAgent whose get_environment_info() returns a non-empty dict has its keys present in the finalized EvaluationResult.environment_info and in the serialized run.json. Every existing test feeds an empty dict or agent=None (tests/test_orchestrator.py:605, :669, tests/test_route_seam_exhaustiveness.py:90), so the update() at orchestrator.py:1217 — the cross-repo contract seam the external eval-runner consumes — has zero coverage; the new marker tests assert only that a method returns its own hardcoded constant. Why not static: The defect class is a lost/overwritten dict merge at runtime plus JSON serialization, not a source pattern — no AST shape distinguishes a merge that survives finalization from one that is later clobbered. Prevents: Finding 5 (tautological marker tests; nothing verifies the marker reaches the run record).
• Producer-built fixtures for cross-repo record fields: add a shared fixture factory that builds sdk_options by calling the real dump_dataclass(ClaudeAgentOptions(...)) and use it in tests/test_reports.py instead of hand-written dicts, plus a golden snapshot of the sdk_options/environment_info slice of run.json checked into the report tests. The guard at tests/test_reports.py:904 (assert "**System Prompt**" not in report_md) still passes only because its fixture hardcodes "system_prompt": None at line 884 — a value a real Claude Code run can no longer produce, since the persisted value is now always a preset dict, which reports.py:90-94 renders into the Markdown/HTML "System Prompt" row as a raw Python dict repr on an unconditionally-present row. Why not static: The drift is in the runtime value shape emitted by a third-party SDK dataclass dump; no lint rule can know that dump_dataclass started returning a dict where a str | None used to be — only a fixture produced by the real producer can. Prevents: Finding 8 (report row renders a dict repr and now always appears; stale hand-built fixture masks it).
• Pin the non-argv half of the SDK contract, or narrow the claim: _transport_command's docstring (tests/test_agent.py:380-386) says it "pins the SDK contract", but exclude_dynamic_sections=True never reaches argv — the SDK lifts it out of the preset dict (claude_agent_sdk/_internal/client.py:148-155) and sends it as request["excludeDynamicSections"] in the control-protocol initialize message (_internal/query.py:209-210). Either assert on that extraction path (drive the options through the SDK's initialize-request builder and check the field) or narrow the docstring to "pins argv only" so the reproducibility claim in docs/agents/CLAUDE_CODE.md is not backed by a test that cannot see it. Why not static: The value travels through a vendored third-party runtime control protocol, and the SDK explicitly notes "older CLIs ignore unknown initialize fields" — whether the flag takes effect is observable only by exercising the SDK, never from our source tree. Prevents: Finding 7 (the reproducibility half of the change is untested while the helper's docstring claims otherwise).
• Simulation-mode wire snapshot: add one test in the user-simulator suite asserting the built ClaudeAgentOptions.system_prompt is the bare persona string (no {'type': 'preset', 'preset': 'claude_code', ...} wrapper). Existing simulator tests assert only on the rendered prompt text (sim.system_prompt), which is why a change that never touched src/coder_eval/simulation/ still silently altered every dialog-mode run's system prompt. Why not static: CE034 enforces that system_prompt_mode is passed explicitly, but not that the chosen value is the correct one for an identity prompt; only inspecting the assembled SDK options shows whether the coding-agent preset prefixes the persona. Prevents: Finding 6 / high (simulator persona shipped behind the Claude Code preset, contradicting its own "stay in character" instruction).

Top 5 Priority Actions

1. Set system_prompt_mode="replace" in the simulator's parse_agent_config(...) call at src/coder_eval/simulation/user_simulator.py:205-214 and enforce the invariant at the shared sub-agent seam (mirroring the setting_sources guard at src/coder_eval/evaluation/sub_agent.py:86) — today the roleplay persona is merely appended to the claude_code preset, changing agent behavior and therefore scores on every simulation: task for identical agent output.
2. Reconcile the two-term regime condition at src/coder_eval/agents/claude_code_agent.py:1192 with the one-term telemetry marker at :1251 by extracting a shared _effective_prompt_mode() helper and adding a @model_validator(mode="after") on ClaudeCodeAgentConfig that rejects system_prompt_mode == "replace" when both system_prompt and system_prompt_file are unset — otherwise -D agent.system_prompt_mode=replace silently runs the full preset while run.json records "replace", mis-bucketing trend dashboards the marker's own docstring says must not pool across that boundary.
3. Teach collect_agent_settings_rows (src/coder_eval/reports.py:90-94) the SystemPromptPreset shape — or unwrap the effective prompt string plus mode before persisting at src/coder_eval/agents/claude_code_agent.py:1218-1229 — since the Markdown and HTML "System Prompt" row now renders a Python dict repr and always appears, with the existing guard at tests/test_reports.py:904 green only because its fixture hardcodes a None a real Claude run can no longer produce.
4. Switch src/coder_eval/agents/antigravity_agent.py:351 from system_instructions=self.config.system_prompt or None to the is not None check used by Claude Code (:1196) and Codex (:1290), so system_prompt: "" is not silently dropped on one agent while forwarded on the other two — or document why the Antigravity SDK requires the truthiness form.
5. Correct the append-only prose the same PR falsified: the absolute "never a replacement" at src/coder_eval/models/agent_config.py:154, the "always kept" row at docs/agents/CLAUDE_CODE.md:102, and the stale "only emits when a custom endpoint is configured" docstring at src/coder_eval/agents/codex_agent.py:940 (the dict is now returned unconditionally), and close the two thin test seams — a replace-with-unset-prompt case and one assertion that an agent-supplied environment_info key survives the merge at src/coder_eval/orchestrator.py:1217.

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Stats: 0 🔴 · 2 🟠 · 2 🟡 · 5 🔵 across 8 axes reviewed.