fix: record Codex edits made through the unified exec tool

[wasabeef]

Summary

• parse nested tools.apply_patch(...) / tools.exec_command(...) calls inside custom_tool_call: exec transcript entries with a bounded JavaScript tokenizer (string literals and comments are skipped, so quoted or commented tool references never attribute)
• extract inline patch text for file attribution and line stats, and treat cmd: string arguments as shell-mutation evidence
• mark nested apply_patch calls as mutating even when the patch text is built dynamically, so commit-level attribution can still recover the commit
• keep direct apply_patch / exec_command transcript formats unchanged

Root cause

Codex CLI 0.142.5 (unified executor) records file edits as JavaScript nested inside custom_tool_call: exec instead of direct apply_patch tool calls. The transcript parser only recognized direct tool calls, so nested edits produced neither files_touched nor mutation evidence, and Agent Note safely declined to write a git note.

User impact

Codex commits made through the unified exec tool now record git notes with file attribution and an AI Ratio in PR Report and Dashboard. Read-only nested calls do not create false-positive attribution.

Validation

• CLI build, typecheck, and lint
• CLI tests: 491 passed (4 new regression tests covering nested patch extraction, nested mutating commands, dynamically built patches, and quoted/commented references)
• End-to-end test records a git note with attribution.method: line and ai_ratio: 100 from a Codex 0.142.5-shaped transcript

Closes #83

🧑💬🤖 Agent Note

Total AI Ratio: █░░░░░░░ 9%
Model: claude-fable-5

Commit	AI Ratio	Prompts	Files
75023aa fix(codex): attribute nested exec tool calls from current Codex transcripts	░░░░░ 7%	2	cli.js 👤, codex.test.ts 🤖, codex.ts 🤖, codex.test.ts 👤
41996c0 refactor(codex): name the nested cmd key regex	█████ 100%	1	cli.js 👤, codex.ts 🤖

Open Dashboard ↗

💬 Prompts & Responses (3 total)

75023aa fix(codex): attribute nested exec tool calls from current Codex transcripts

🧑 Prompt

M packages/cli/dist/cli.js
M packages/cli/src/agents/codex.test.ts
M packages/cli/src/agents/codex.ts
M packages/cli/src/commands/codex.test.ts

の変更を確認してほしい。

#83

の修正した

🧑 Prompt

修正が必要なものは修正作業を行ってから PR 作成してほしい

41996c0 refactor(codex): name the nested cmd key regex

🧑 Prompt

#85 (comment)

Summary by CodeRabbit

• New Features

  • Improved Codex transcript handling to recognize nested tool usage inside exec calls.
  • Better reports now include nested tools like patching and command execution when they appear in wrapped transcripts.

• Bug Fixes

  • File-change and line-attribution details are now captured more reliably for nested patch content.
  • Read-only or quoted tool mentions are no longer misclassified as mutations.
  • Nested patch and command activity is now reflected more accurately in notes and interaction summaries.

[coderabbitai]

📝 Walkthrough

Walkthrough

This PR adds static-analysis recovery of nested tool calls (tools.apply_patch, tools.exec_command) embedded in JavaScript source passed to Codex's exec tool invocations. extractInteractions now attributes nested tools, mutation markers, and file/line evidence accordingly, with new unit and integration test coverage.

Changes

Nested exec tool call attribution

Layer / File(s)	Summary
Nested evidence recovery utilities packages/cli/src/agents/codex.ts	New helper functions scan exec source text for tools.apply_patch(...) and tools.exec_command(...) calls and extract string-literal patch/command inputs.
Interaction extraction wiring packages/cli/src/agents/codex.ts	extractInteractions computes nested exec evidence, appends nested tool names, marks apply_patch/exec_command as mutating, and derives patchInputs for file/line-stat attribution from nested evidence.
Unit tests for nested attribution packages/cli/src/agents/codex.test.ts	New buildNestedExecTranscript helper and tests cover static patch text, dynamic patch text, mutating exec_command, and quoted/commented false-positive avoidance.
Integration test for hook flow packages/cli/src/commands/codex.test.ts	New buildNestedExecPatchTranscript helper and an end-to-end test verify git-note attribution, ai_ratio, files_touched, and tools list from a nested exec transcript.

Estimated code review effort: 3 (Moderate) | ~25 minutes

Sequence Diagram(s)

sequenceDiagram
  participant Transcript
  participant extractInteractions
  participant NestedEvidenceHelper
  participant Interaction
  participant GitNote

  Transcript->>extractInteractions: custom_tool_call "exec" with input source
  extractInteractions->>NestedEvidenceHelper: scan source for tools.apply_patch/exec_command
  NestedEvidenceHelper-->>extractInteractions: nested tool names, patch/command inputs
  extractInteractions->>Interaction: append nested tools & mutation markers
  extractInteractions->>Interaction: attribute files_touched/line_stats
  Interaction->>GitNote: record ai_ratio and file attribution

Loading

Possibly related PRs

• wasabeef/AgentNote#72: Both PRs modify packages/cli/src/agents/codex.ts transcript interaction extraction around exec/apply_patch evidence and mutation tagging, extended here to nested exec tool calls.

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Linked Issues check	✅ Passed	The code and tests address nested exec transcripts, preserve direct tool support, and cover false-positive avoidance and AI ratio attribution.
Out of Scope Changes check	✅ Passed	The changes stay focused on nested exec attribution and regression tests, with no clear unrelated additions.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title clearly summarizes the main change: recording Codex edits made through the unified exec tool.

✨ Finishing Touches

📝 Generate docstrings

• Create stacked PR
• Commit on current branch

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch fix/issue-83-codex-nested-exec

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[coderabbitai]

Actionable comments posted: 1

🤖 Prompt for all review comments with AI agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Inline comments:
In `@packages/cli/src/agents/codex.ts`:
- Around line 249-256: The inline regex inside the stringLiterals filter in
codex.ts should be hoisted into a named module-level const with a short intent
comment, matching the existing style of SHELL_MUTATION_COMMAND_RE. Move the
`cmd:`/quoted `cmd` key matcher out of the callback, give it a descriptive name
like NESTED_CMD_KEY_RE, and update the filter in commandInputs to reference that
constant so the mutation-evidence heuristic is easier to read and maintain.

🪄 Autofix (Beta)

Fix all unresolved CodeRabbit comments on this PR:

• Push a commit to this branch (recommended)
• Create a new PR with the fixes

---

ℹ️ Review info

⚙️ Run configuration

Configuration used: Path: .coderabbit.yaml

Review profile: ASSERTIVE

Plan: Pro Plus

Run ID: 451e7b86-640e-4aa9-8dd1-c24ca07777e7

📥 Commits

Reviewing files that changed from the base of the PR and between 0b9201a and 75023aa.

⛔ Files ignored due to path filters (1)

• packages/cli/dist/cli.js is excluded by !**/dist/**, !**/dist/**

📒 Files selected for processing (3)

• packages/cli/src/agents/codex.test.ts
• packages/cli/src/agents/codex.ts
• packages/cli/src/commands/codex.test.ts