fix: isolate system prompt via AGENTS.md for Codex and OpenCode

[akashgit]

Summary

Fixes #471 — system prompt exposure in non-Claude runners.

• Codex: System prompt is now written to a temporary AGENTS.md in the project directory. Codex auto-reads it as system-level instructions. Only the task is passed as the user message. Original AGENTS.md is backed up and restored in a finally block.
• OpenCode: Same approach — OpenCode also reads AGENTS.md for system instructions. Prompt goes to AGENTS.md, only the task is passed via -p.
• Bob: Left as concatenation — no known mechanism for separate system prompt delivery.

Before

All non-Claude runners dumped the full 2000+ line factory CEO prompt at the start of every session as part of the user message.

After

The system prompt is invisible to the user (loaded via AGENTS.md). Only the task appears as the user message.

Test plan

• uv run pytest tests/test_codex_runner.py tests/test_runners.py -v — 99 passed
• uv run pytest tests/ -x -q --tb=short -m "not slow" — 2211 passed, 3 skipped
• uv run ruff check — all checks passed
• AGENTS.md lifecycle tests: creation, append to existing, cleanup, restore

🤖 Generated with Claude Code

[codecov]

Codecov Report

❌ Patch coverage is 81.48148% with 15 lines in your changes missing coverage. Please review.
✅ Project coverage is 86.77%. Comparing base (61d86a7) to head (fe45e96).
⚠️ Report is 11 commits behind head on main.

Files with missing lines	Patch %	Lines
factory/runners/opencode.py	63.63%	12 Missing ⚠️
factory/runners/codex.py	93.75%	3 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #501      +/-   ##
==========================================
- Coverage   86.94%   86.77%   -0.18%     
==========================================
  Files          64       64              
  Lines        9937    10013      +76     
==========================================
+ Hits         8640     8689      +49     
- Misses       1297     1324      +27     

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[gx-ai-architect]

@ceo review

[gx-ai-architect]

@ceo-review

[github-actions]

❌ Factory Review: REVERT

Verdict: REVERT
Reason: Critical mypy type error: instance attributes _agents_md_path and _agents_md_backup assigned None without explicit Path | None type annotation in both CodexRunner and OpenCodeRunner classes. Type safety violation blocks merge.

---

Posted by Factory CEO

[gx-ai-architect]

@ceo-review redo the review, while also share the test you have run if you were to approve

[github-actions]

❌ Factory Review: REVERT

Verdict: REVERT
Reason: Critical exception handling bugs — AGENTS.md can be left corrupted if file operations throw before try-finally block is entered

---

Posted by Factory CEO

[gx-ai-architect]

@ceo-review

[github-actions]

❌ Factory Review: REVERT

Verdict: REVERT
Reason: Critical race condition in concurrent agent invocations — multiple agents modifying shared AGENTS.md causes data corruption

Guard Checks

Check	Result
scope	✅ PASS
no_eval_changes	✅ PASS

Code Review Notes

• CRITICAL: Race condition on shared AGENTS.md file in concurrent invocations
• IMPORTANT: No atomic file operations — needs file locking
• IMPORTANT: Silent cleanup failure — OSError logged at DEBUG only
• IMPORTANT: Encoding not specified — use explicit UTF-8
• MINOR: Defensive getattr unnecessary

---

Posted by Factory CEO

[github-actions]

CEO Code Review — Detailed Findings

Summary

PR #501 fixes issue #471 (system prompt exposure) but introduces a critical race condition that breaks concurrent agent execution. Tests pass (99/99) but do not cover the concurrent invocation scenario that would trigger the bug in production.

---

Critical Issue: Race Condition on Shared AGENTS.md

Location: factory/runners/codex.py:104-106, factory/runners/opencode.py:115-117

Problem: The runners use instance variables (_agents_md_path, _agents_md_backup) to track state, but get_runner() creates a fresh instance per invocation. When multiple agents run concurrently on the same project (via invoke_agents_parallel()), they ALL modify the same project_dir/AGENTS.md file without synchronization.

Impact:

• Lost writes: Agent A writes prompt A → Agent B overwrites with prompt B → Agent A's cleanup restores wrong backup
• File corruption: Interleaved writes during append operations
• Permanent data loss: If Agent B creates AGENTS.md while Agent A is running with a backup, A's cleanup deletes B's content

Evidence:

# factory/agents/runner.py:288
async def invoke_agents_parallel(tasks, project_path, ...):
    coros = [invoke_agent(role, task, project_path, ...) for role, task in tasks]
    results = list(await asyncio.gather(*coros))  # Concurrent execution

CEO prompt documents parallel execution (lines 1254-1271):

"For hypotheses with non-overlapping file scopes, execute them in parallel"

Why tests didn't catch it:

• All tests run sequentially with isolated temp directories
• No test case covers 2+ agents running concurrently on the same project

---

Important Issues

1. No atomic file operations (codex.py:126, opencode.py:143)

   • Pattern: read → write (backup or new) → restore
   • Between read and write, another process could modify the file
   • Fix: Use filelock.FileLock or fcntl.flock

2. Silent cleanup failure (codex.py:199, opencode.py:196)

   • OSError during _restore_agents_md() is only logged at DEBUG level
   • If cleanup fails (disk full, permissions), system prompt leaks on disk permanently
   • Fix: Log at WARNING level minimum, or bubble up the exception

3. Encoding not specified (codex.py:125-127, opencode.py:142-144)

   • read_text()/write_text() use system default encoding
   • Non-UTF-8 content in original AGENTS.md or prompt could corrupt data
   • Fix: Use explicit encoding='utf-8' on all file operations

---

Recommended Fixes (pick one approach)

Option 1: Process-level locking (recommended)

from filelock import FileLock

def _setup_agents_md(self, cwd: Path, prompt: str) -> None:
    agents_md = cwd / "AGENTS.md"
    lock_path = cwd / ".factory" / "agents_md.lock"
    
    self._lock = FileLock(lock_path, timeout=30)
    self._lock.acquire()
    
    self._agents_md_path = agents_md
    if agents_md.is_file():
        self._agents_md_backup = agents_md.read_text(encoding='utf-8')
        agents_md.write_text(f"{self._agents_md_backup}\n\n{prompt}", encoding='utf-8')
    else:
        self._agents_md_backup = None
        agents_md.write_text(prompt, encoding='utf-8')

def _restore_agents_md(self) -> None:
    try:
        if self._agents_md_backup is not None:
            self._agents_md_path.write_text(self._agents_md_backup, encoding='utf-8')
        elif self._agents_md_path.is_file():
            self._agents_md_path.unlink()
    except OSError:
        log.warning("agents_md_restore_failed", exc_info=True)  # Warning, not debug
    finally:
        if hasattr(self, '_lock'):
            self._lock.release()

Option 2: Per-agent temp files

Write to AGENTS.md.<role>.<pid> instead of shared AGENTS.md. Requires confirming Codex/OpenCode support this naming pattern.

Option 3: Serial execution only

Document that Codex/OpenCode runners do not support parallel invocation. Enforce at invoke_agents_parallel level (skip or serialize).

---

Test Coverage Gaps

The PR added comprehensive happy-path tests but missed:

• ❌ Concurrent invocations (2+ agents on same project)
• ❌ Encoding edge cases (non-UTF-8 AGENTS.md content)
• ❌ Cleanup failure scenarios (disk full, permissions denied)

---

Next Steps

Before re-submitting:

1. Add process-level file locking to prevent race conditions
2. Specify encoding='utf-8' on all file operations
3. Log cleanup failures at WARNING level minimum
4. Add a concurrent invocation test case
5. Update CLAUDE.md to document the locking mechanism

cc @akashgit

[osilkin98]

✅ Factory Review: KEEP

Verdict: KEEP
Reason: PR correctly solves issue #471 (system prompt exposure in non-Claude runners) with solid test coverage and no regressions; all three prior claims are confirmed as real design gaps but none are blocking — they are hardening follow-ups, not merge blockers.

Hypothesis: Isolate system prompt via AGENTS.md for Codex and OpenCode runners (issue #471)

Precheck Gate

3 claims adjudicated: 3 confirmed (all non-blocking). 2 additional findings.

Code Review Notes

• These numbered claims came from a pre-review triage pass using the Claude Fable model. This CEO review independently verified or refuted each one against the code. Proposed as standard practice in issue #517.
• CLAIM 1 CONFIRMED (non-blocking): Double-backup poisoning on hard process death. If the process is SIGKILLed, OOM-killed, or tmux-killed after _setup_agents_md writes AGENTS.md but before _restore_agents_md runs, the factory-written content remains on disk. The next run treats it as the user's original and backs it up, permanently destroying the real file. Verified: grep confirms zero sentinel markers in written content, zero startup recovery paths. The fix commit (fe45e96) narrowed the exception-gap (moved write adjacent to try-finally from being 5 lines away in build_command), but does NOT address SIGKILL — Python finally blocks do not run on SIGKILL. Why it matters: a user's project AGENTS.md could be silently replaced with a 2000-line factory CEO prompt after a hard crash. Mitigation suggestion: add a sentinel comment (e.g. '# factory:system-prompt-start') and strip on startup.
• CLAIM 2 CONFIRMED (non-blocking): Concurrent factory runs race on AGENTS.md. The backup lives in instance state (self._agents_md_backup), and get_runner() at factory/runners/init.py:70 creates a fresh instance per invoke_agent() call. Two separate 'factory ceo' processes targeting the same project directory would race on read-write of the same AGENTS.md. Verified: no file-level locking exists around AGENTS.md (filelock is only used in store.py for experiment IDs and TSV writes). Why it matters: in practice, running two CEO processes against the same directory is not a supported use case and the factory already lacks concurrency guards at every other level. This is a pre-existing architectural gap, not a regression from this PR.
• CLAIM 3 CONFIRMED (non-blocking): _setup_agents_md and _restore_agents_md are copy-pasted between codex.py and opencode.py. Verified by diff: _setup_agents_md is byte-identical across both files. _restore_agents_md differs only in docstring noun, log event name, and one inconsistency — codex.py:190 uses getattr(self, '_agents_md_path', None) while opencode.py:148 uses self._agents_md_path directly. Both work because class-level annotations initialize the attributes, but the defensive-vs-direct inconsistency is a code smell. Why it matters: any future bug fix must land in two places. Extract to a shared mixin or factory/runners/_agents_md.py helper.
• ADDITIONAL: _setup_agents_md() is called OUTSIDE the try block in all 4 methods (codex.py headless:162 before try:163, codex.py interactive:213 before try:214, opencode.py headless:185 before try:186, opencode.py interactive:205 before try:206). If _setup_agents_md itself raises (e.g. PermissionError), _restore_agents_md will not run. Why it matters: low practical impact since a failed write leaves inconsistent backup state anyway, but moving the call inside the try block would be strictly more correct.
• ADDITIONAL: No test regressions. 2206 tests pass, 3 skipped. 5 failures in test_cli.py (TestCmdCeoInteractive, TestCmdCeoResearchIdeation) are pre-existing on main, verified by checkout. Lint (ruff) and type checks (mypy) clean on all changed files.

---

Posted by Factory CEO

[osilkin98]

For reference, same setup as #514: I ran the open PR backlog through the Claude Fable model as a triage pass, and it flagged 3 issues on this PR. The CEO review above adjudicated each one independently (confirmed all 3, judged them non-blocking). The original claims it was given, verbatim:

1. Double-backup poisoning: if the process dies without running finally (SIGKILL, tmux kill, OOM), the factory-written AGENTS.md remains in the user's repo; the NEXT run's _setup_agents_md treats it as the user's original and backs it up, permanently destroying the real file. There is no sentinel marker identifying factory-written AGENTS.md and no startup recovery path.
2. Concurrent factory runs against the same project race on backup/restore: the backup lives in instance state (self._agents_md_backup), so two runners can clobber each other's view of the "original".
3. _setup_agents_md and _restore_agents_md are copy-pasted verbatim between codex.py and opencode.py, so any fix must land twice; extract shared helpers.

Follow-up work is tracked in #518. Process proposal for making this a standard part of CEO review is #517.

[osilkin98]

One correction to my review above. The CEO detailed review from Jun 7 in this thread rated the AGENTS.md race as critical, with a concrete trigger path: invoke_agents_parallel() runs agents concurrently within a single factory run, so this doesn't need two separate factory processes to happen. My review called it non-blocking on the assumption that concurrent runs against one project aren't a supported use case, and that finding undercuts the assumption. I've updated #518 to track the fix (file locking around AGENTS.md setup/restore; filelock is already a dependency). If folks think this makes it a merge blocker rather than a follow-up, no objection from me.