trace-to-skill 0.1.40 → 0.1.42

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Files changed (17) hide show
  1. package/README.md +5 -3
  2. package/dist/src/benchmark.js +6 -0
  3. package/dist/src/benchmark.js.map +1 -1
  4. package/dist/src/rules.js +21 -1
  5. package/dist/src/rules.js.map +1 -1
  6. package/dist/src/types.d.ts +1 -1
  7. package/docs/BENCHMARK.md +1 -0
  8. package/docs/CODEX_ISSUE_MAP.md +3 -0
  9. package/docs/DISCOVERY.md +1 -1
  10. package/docs/FAILURE_TAXONOMY.md +8 -0
  11. package/docs/RELEASE.md +1 -1
  12. package/docs/SCORECARD.md +2 -1
  13. package/docs/USE_CASES.md +1 -1
  14. package/fixtures/codex-tool-call-integrity.md +34 -0
  15. package/llms.txt +1 -1
  16. package/package.json +3 -1
  17. package/schemas/analysis-result.schema.json +1 -0
package/README.md CHANGED
@@ -53,6 +53,7 @@ Use it when you need to:
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  - **Debug Codex resume/session state:** run `trace-to-skill analyze ./runs` when `codex resume` freezes, large JSONL histories make Desktop sluggish, recent context disappears after resume, or SQLite migration/state errors break goals.
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  - **Attribute token burn:** run `trace-to-skill analyze ./runs` when Codex drains usage unexpectedly because of background polling, idle app activity, compaction loops, retry spirals, fast-mode drift, or cached-token-heavy turns.
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  - **Report resource leaks:** run `trace-to-skill analyze ./runs` when Codex Desktop, VS Code extension, app-server, renderer, GPU, or orphaned helper processes keep burning CPU/GPU/memory after the work should be idle.
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+ - **Catch tool-call integrity failures:** run `trace-to-skill analyze ./runs` when `apply_patch`, rollback/undo, subagent shutdown, or `tool_call_id` protocol failures threaten file safety or strand a session.
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  - **File better OpenAI/Codex issues:** run `trace-to-skill codex-report ./runs` to turn a failed trace into a redaction-aware, copy-paste-ready issue body with evidence and diagnostics.
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  - **Package quota bugs cleanly:** run `trace-to-skill analyze ./runs` on Codex traces where `/status` or the usage page shows remaining quota but the client returns `You've hit your usage limit`.
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@@ -150,6 +151,7 @@ Trace analysis detects run-level failures:
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  | Codex session state | Resume, history rendering, context compression, archived chats, or local SQLite/global-state migrations break long sessions |
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  | Codex token burn | Background polling, idle app activity, compaction/replay, cached-token-heavy turns, or retry loops drain usage unexpectedly |
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  | Codex resource leak | Desktop/app/extension/helper processes, shell snapshots, renderer, GPU, or log loops keep consuming local resources |
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+ | Codex tool-call integrity | Patch safety, rollback/undo, subagent shutdown, or missing tool-call responses break maintainer trust |
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  | Quota mismatch | Codex usage dashboard, `/status`, account state, or reset timing contradicts a usage-limit block |
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  | MCP risk | Tool permissions and trust boundaries are unclear |
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@@ -353,7 +355,7 @@ jobs:
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  issues: write
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  steps:
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  - uses: actions/checkout@v5
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- - uses: grnbtqdbyx-create/trace-to-skill@v0.1.40
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+ - uses: grnbtqdbyx-create/trace-to-skill@v0.1.42
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  with:
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  mode: all
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  doctor-threshold: "85"
@@ -402,7 +404,7 @@ Composite action usage:
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  ```yaml
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  - id: trace-to-skill
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- uses: grnbtqdbyx-create/trace-to-skill@v0.1.40
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+ uses: grnbtqdbyx-create/trace-to-skill@v0.1.42
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  with:
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  mode: all
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  doctor-threshold: "85"
@@ -444,7 +446,7 @@ Action outputs:
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  By default, generated reports are also appended to the GitHub Actions Job Summary. Set `job-summary: "false"` to disable that UI output.
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- Tagged Action releases build and run the CLI from `$GITHUB_ACTION_PATH`, so a workflow pinned to a release tag such as `@v0.1.40` executes that release's checked-out source instead of pulling the default branch at runtime.
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+ Tagged Action releases build and run the CLI from `$GITHUB_ACTION_PATH`, so a workflow pinned to a release tag such as `@v0.1.42` executes that release's checked-out source instead of pulling the default branch at runtime.
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  ## Codex Skill
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package/dist/src/benchmark.js CHANGED
@@ -90,6 +90,12 @@ const BENCHMARK_CASES = [
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  fixture: "fixtures/codex-resource-leak.md",
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  expectedKinds: ["codex_resource_leak", "weak_evidence"]
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  },
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+ {
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+ id: "codex-tool-call-integrity",
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+ title: "Codex tool-call integrity and rollback failure",
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+ fixture: "fixtures/codex-tool-call-integrity.md",
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+ expectedKinds: ["codex_tool_call_integrity", "weak_evidence"]
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+ },
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  {
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  id: "prompt-injection",
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  title: "Untrusted PR comment prompt injection",
package/dist/src/benchmark.js.map CHANGED
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1
+ {"version":3,"file":"benchmark.js","sourceRoot":"","sources":["../../src/benchmark.ts"],"names":[],"mappings":"AAAA,OAAO,IAAI,MAAM,WAAW,CAAC;AAC7B,OAAO,EAAE,aAAa,EAAE,MAAM,UAAU,CAAC;AACzC,OAAO,EAAE,cAAc,EAAE,MAAM,cAAc,CAAC;AA8B9C,MAAM,eAAe,GAA8B;IACjD;QACE,EAAE,EAAE,qBAAqB;QACzB,KAAK,EAAE,2BAA2B;QAClC,OAAO,EAAE,sBAAsB;QAC/B,aAAa,EAAE,EAAE;QACjB,YAAY,EAAE,IAAI;KACnB;IACD;QACE,EAAE,EAAE,iBAAiB;QACrB,KAAK,EAAE,yCAAyC;QAChD,OAAO,EAAE,wBAAwB;QACjC,aAAa,EAAE,CAAC,cAAc,EAAE,sBAAsB,EAAE,eAAe,EAAE,UAAU,EAAE,mBAAmB,CAAC;QACzG,eAAe,EAAE,IAAI;KACtB;IACD;QACE,EAAE,EAAE,aAAa;QACjB,KAAK,EAAE,4BAA4B;QACnC,OAAO,EAAE,8BAA8B;QACvC,aAAa,EAAE,CAAC,cAAc,EAAE,sBAAsB,EAAE,eAAe,CAAC;QACxE,eAAe,EAAE,IAAI;KACtB;IACD;QACE,EAAE,EAAE,oBAAoB;QACxB,KAAK,EAAE,kCAAkC;QACzC,OAAO,EAAE,gCAAgC;QACzC,aAAa,EAAE,CAAC,oBAAoB,EAAE,eAAe,CAAC;KACvD;IACD;QACE,EAAE,EAAE,oBAAoB;QACxB,KAAK,EAAE,kCAAkC;QACzC,OAAO,EAAE,gCAAgC;QACzC,aAAa,EAAE,CAAC,oBAAoB,EAAE,eAAe,CAAC;KACvD;IACD;QACE,EAAE,EAAE,oBAAoB;QACxB,KAAK,EAAE,qCAAqC;QAC5C,OAAO,EAAE,gCAAgC;QACzC,aAAa,EAAE,CAAC,oBAAoB,EAAE,eAAe,CAAC;KACvD;IACD;QACE,EAAE,EAAE,sBAAsB;QAC1B,KAAK,EAAE,2CAA2C;QAClD,OAAO,EAAE,kCAAkC;QAC3C,aAAa,EAAE,CAAC,sBAAsB,EAAE,eAAe,CAAC;KACzD;IACD;QACE,EAAE,EAAE,gBAAgB;QACpB,KAAK,EAAE,sBAAsB;QAC7B,OAAO,EAAE,4BAA4B;QACrC,aAAa,EAAE,CAAC,gBAAgB,EAAE,eAAe,CAAC;KACnD;IACD;QACE,EAAE,EAAE,UAAU;QACd,KAAK,EAAE,iCAAiC;QACxC,OAAO,EAAE,wBAAwB;QACjC,aAAa,EAAE,CAAC,iBAAiB,EAAE,UAAU,CAAC;QAC9C,eAAe,EAAE,IAAI;KACtB;IACD;QACE,EAAE,EAAE,uBAAuB;QAC3B,KAAK,EAAE,wCAAwC;QAC/C,OAAO,EAAE,mCAAmC;QAC5C,aAAa,EAAE,CAAC,uBAAuB,EAAE,eAAe,CAAC;KAC1D;IACD;QACE,EAAE,EAAE,mBAAmB;QACvB,KAAK,EAAE,2BAA2B;QAClC,OAAO,EAAE,+BAA+B;QACxC,aAAa,EAAE,CAAC,mBAAmB,EAAE,eAAe,CAAC;KACtD;IACD;QACE,EAAE,EAAE,qBAAqB;QACzB,KAAK,EAAE,wCAAwC;QAC/C,OAAO,EAAE,iCAAiC;QAC1C,aAAa,EAAE,CAAC,qBAAqB,EAAE,eAAe,CAAC;KACxD;IACD;QACE,EAAE,EAAE,kBAAkB;QACtB,KAAK,EAAE,uCAAuC;QAC9C,OAAO,EAAE,8BAA8B;QACvC,aAAa,EAAE,CAAC,kBAAkB,EAAE,eAAe,CAAC;KACrD;IACD;QACE,EAAE,EAAE,qBAAqB;QACzB,KAAK,EAAE,yCAAyC;QAChD,OAAO,EAAE,iCAAiC;QAC1C,aAAa,EAAE,CAAC,qBAAqB,EAAE,eAAe,CAAC;KACxD;IACD;QACE,EAAE,EAAE,2BAA2B;QAC/B,KAAK,EAAE,gDAAgD;QACvD,OAAO,EAAE,uCAAuC;QAChD,aAAa,EAAE,CAAC,2BAA2B,EAAE,eAAe,CAAC;KAC9D;IACD;QACE,EAAE,EAAE,kBAAkB;QACtB,KAAK,EAAE,uCAAuC;QAC9C,OAAO,EAAE,8BAA8B;QACvC,aAAa,EAAE,CAAC,kBAAkB,CAAC;QACnC,eAAe,EAAE,IAAI;KACtB;IACD;QACE,EAAE,EAAE,mBAAmB;QACvB,KAAK,EAAE,qCAAqC;QAC5C,OAAO,EAAE,4BAA4B;QACrC,aAAa,EAAE,CAAC,qBAAqB,CAAC;KACvC;CACF,CAAC;AAEF,MAAM,CAAC,KAAK,UAAU,YAAY;IAChC,MAAM,KAAK,GAA0B,EAAE,CAAC;IACxC,MAAM,IAAI,GAAG,WAAW,EAAE,CAAC;IAE3B,KAAK,MAAM,UAAU,IAAI,eAAe,EAAE,CAAC;QACzC,MAAM,MAAM,GAAG,MAAM,cAAc,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,UAAU,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC;QAC3E,MAAM,aAAa,GAAG,KAAK,CAAC,IAAI,CAAC,IAAI,GAAG,CAAC,MAAM,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,OAAO,EAAE,EAAE,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;QACjG,MAAM,gBAAgB,GAAG,MAAM,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC,OAAO,EAAE,EAAE,CAAC,OAAO,CAAC,QAAQ,KAAK,UAAU,CAAC,CAAC,MAAM,CAAC;QAErG,KAAK,CAAC,IAAI,CAAC;YACT,EAAE,EAAE,UAAU,CAAC,EAAE;YACjB,KAAK,EAAE,UAAU,CAAC,KAAK;YACvB,OAAO,EAAE,UAAU,CAAC,OAAO;YAC3B,KAAK,EAAE,MAAM,CAAC,KAAK;YACnB,QAAQ,EAAE,MAAM,CAAC,QAAQ,CAAC,MAAM;YAChC,gBAAgB;YAChB,aAAa;YACb,aAAa,EAAE,UAAU,CAAC,aAAa;YACvC,MAAM,EAAE,UAAU,CAAC,UAAU,EAAE,aAAa,EAAE,MAAM,CAAC,QAAQ,CAAC,MAAM,EAAE,gBAAgB,CAAC;SACxF,CAAC,CAAC;IACL,CAAC;IAED,OAAO;QACL,WAAW,EAAE,IAAI,IAAI,EAAE,CAAC,WAAW,EAAE;QACrC,MAAM,EAAE,KAAK,CAAC,KAAK,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,MAAM,CAAC;QAC1C,KAAK;KACN,CAAC;AACJ,CAAC;AAED,MAAM,UAAU,uBAAuB,CAAC,MAAuB;IAC7D,MAAM,KAAK,GAAG;QACZ,4BAA4B;QAC5B,EAAE;QACF,aAAa,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,MAAM,IAAI;QAChD,EAAE;QACF,8OAA8O;QAC9O,EAAE;QACF,4EAA4E;QAC5E,gDAAgD;KACjD,CAAC;IAEF,KAAK,MAAM,IAAI,IAAI,MAAM,CAAC,KAAK,EAAE,CAAC;QAChC,KAAK,CAAC,IAAI,CAAC;YACT,KAAK,IAAI,CAAC,KAAK,EAAE;YACjB,KAAK,IAAI,CAAC,OAAO,IAAI;YACrB,GAAG,IAAI,CAAC,KAAK,EAAE;YACf,GAAG,IAAI,CAAC,QAAQ,EAAE;YAClB,GAAG,IAAI,CAAC,gBAAgB,EAAE;YAC1B,IAAI,CAAC,aAAa,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,aAAa,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,KAAK,IAAI,IAAI,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,MAAM;YACnG,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,QAAQ;SAClC,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC;IACjB,CAAC;IAED,KAAK,CAAC,IAAI,CACR,EAAE,EACF,iBAAiB,EACjB,EAAE,EACF,SAAS,EACT,0BAA0B,EAC1B,wCAAwC,EACxC,KAAK,EACL,EAAE,CACH,CAAC;IAEF,OAAO,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;AAC1B,CAAC;AAED,SAAS,UAAU,CACjB,UAAmC,EACnC,aAA4B,EAC5B,QAAgB,EAChB,gBAAwB;IAExB,IAAI,UAAU,CAAC,YAAY,IAAI,QAAQ,KAAK,CAAC,EAAE,CAAC;QAC9C,OAAO,KAAK,CAAC;IACf,CAAC;IAED,IAAI,UAAU,CAAC,eAAe,IAAI,gBAAgB,KAAK,CAAC,EAAE,CAAC;QACzD,OAAO,KAAK,CAAC;IACf,CAAC;IAED,OAAO,UAAU,CAAC,aAAa,CAAC,KAAK,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,aAAa,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC;AAChF,CAAC;AAED,SAAS,WAAW;IAClB,OAAO,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,OAAO,CAAC,aAAa,CAAC,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,OAAO,CAAC,CAAC;AAC7E,CAAC"}
package/dist/src/rules.js CHANGED
@@ -280,7 +280,7 @@ const RULES = [
280
280
  /\b(Code Helper \(Renderer\)|Code Helper \(Plugin\)|Codex Helper Renderer|Codex app-server|syspolicyd|zygote|WindowServer).{0,180}\b(9\d|100|1\d\d|2\d\d|3\d\d)%/i,
281
281
  /\borphaned\b.{0,160}\b(shell[- ]snapshot|zsh|codex|native process|subprocess|helper|process)\b/i,
282
282
  /\b(shell[- ]snapshot|print '# Snapshot file'|\.codex\/shell_snapshots|chat_processes\.json)\b.{0,180}\b(orphan|PPID\s*1|launchd|97%|98%|99%|100%|CPU|spinning|burning)\b/i,
283
- /\b(memory leak|RAM leak|renderer growth|GPU memory|IOSurface|IOAccelerator|resource leak|log flood|repeated warning loop|error flood)\b/i,
283
+ /\b(Codex|app|extension|renderer|GPU|process|helper|log|WindowServer|Code Helper)\b.{0,160}\b(memory leak|RAM leak|renderer growth|GPU memory|IOSurface|IOAccelerator|log flood|repeated warning loop|error flood)\b/i,
284
284
  /\b(thread-stream-state-changed|worker_rpc_response_error|open-in-target not supported|local-environments is not supported|stable-metadata)\b.{0,180}\b(loop|repeated|thousands|high CPU|flood|no handler|error=\{\})\b/i,
285
285
  /\bthinking\b.{0,120}\b(animation|spinner|shimmer)\b.{0,160}\b(GPU|compositor|VSync|reduce motion|70%|100%|battery|power)\b/i,
286
286
  /\b(non[- ]?Git workspace|without \.git|not a Git repository|git repository root)\b.{0,180}\b(high CPU|renderer|Code Helper|runaway|CPU drops|CPU high)\b/i,
@@ -289,6 +289,26 @@ const RULES = [
289
289
  suggestedRule: "When reporting Codex resource leaks, capture app/extension/CLI version, OS, IDE, thread type, exact process names and PIDs, CPU/GPU/RSS samples over time, whether the process is orphaned or PPID 1, log-loop signatures, workspace git-root state, visible animations/reduce-motion state, reproduction steps, and whether closing the panel/app, killing specific PIDs, git init, rollback, or restart clears the leak.",
290
290
  suggestedSkill: "codex-resource-leak-triage"
291
291
  },
292
+ {
293
+ kind: "codex_tool_call_integrity",
294
+ severity: "high",
295
+ title: "Codex tool-call integrity or rollback failure",
296
+ why: "Patch, rollback, subagent, and protocol-level tool-call failures can silently overwrite files, strand threads, or make recovery actions fail unless reports preserve exact tool inputs, tool results, durable state, and recovery evidence.",
297
+ patterns: [
298
+ /\bapply_patch\b.{0,120}\bAdd File\b.{0,160}\b(overwrite|overwrites|existing file|already exists|silently|symlink|replaces? its contents|should fail)\b/i,
299
+ /\b\*\*\* Add File:\b.{0,180}\b(existing file|overwrite|symlink|\.env|target already existed|replaced|destructive)\b/i,
300
+ /\bassistant message with ['"]tool_calls['"] must be followed by tool messages\b/i,
301
+ /\binsufficient tool messages following tool_calls message\b/i,
302
+ /\btool_call_id\b.{0,160}\b(missing|unmatched|not followed|protocol|invalid_request_error|tool messages?)\b/i,
303
+ /\bclose_agent\b.{0,180}\b(hang forever|waits? forever|never returns|thread never terminates|agent thread limit reached|registry slot|already closed)\b/i,
304
+ /\b(subagent|child thread|durable spawn edge|thread_spawn_edges)\b.{0,180}\b(closed|interrupted|terminated|registry slot|thread limit|hang|timeout)\b/i,
305
+ /\b(failed to revert changes|revert changes failed|undo button stopped working|could not undo|rollback failed)\b/i,
306
+ /\b(Codex|agent|extension)\b.{0,180}\b(deleted|truncated|overwrote|destroyed|lost)\b.{0,160}\b(uncommitted code|existing file|codebase|file contents)\b/i,
307
+ /\b(IDE-integrated diff|presenting changes|proposed changes|diff approval|show a diff|apply changes)\b.{0,180}\b(fail|missing|unsafe|rollback|revert|approval)\b/i
308
+ ],
309
+ suggestedRule: "When reporting Codex tool-call integrity failures, capture the exact tool input and output, app/CLI/extension version, OS/IDE, workspace git state, affected file path and whether it already existed or was a symlink, diff before/after, tool_call_id sequence, durable thread state for subagents, rollback/revert attempts, and whether a clean repo reproduction fails the same way.",
310
+ suggestedSkill: "codex-tool-call-integrity-triage"
311
+ },
292
312
  {
293
313
  kind: "quota_mismatch",
294
314
  severity: "high",
package/dist/src/rules.js.map CHANGED
@@ -1 +1 @@
1
- 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package/dist/src/types.d.ts CHANGED
@@ -1,5 +1,5 @@
1
1
  export type Severity = "low" | "medium" | "high" | "critical";
2
- export type FindingKind = "premature_completion" | "tests_not_run" | "test_failure" | "ignored_instruction" | "hallucinated_file" | "over_editing" | "unsafe_command" | "secret_exposure" | "sensitive_file_access" | "hidden_unicode" | "prompt_injection" | "context_compaction" | "sandbox_permission" | "codex_connectivity" | "codex_remote_control" | "codex_mcp_runtime" | "codex_session_state" | "codex_token_burn" | "codex_resource_leak" | "quota_mismatch" | "mcp_risk" | "weak_evidence";
2
+ export type FindingKind = "premature_completion" | "tests_not_run" | "test_failure" | "ignored_instruction" | "hallucinated_file" | "over_editing" | "unsafe_command" | "secret_exposure" | "sensitive_file_access" | "hidden_unicode" | "prompt_injection" | "context_compaction" | "sandbox_permission" | "codex_connectivity" | "codex_remote_control" | "codex_mcp_runtime" | "codex_session_state" | "codex_token_burn" | "codex_resource_leak" | "codex_tool_call_integrity" | "quota_mismatch" | "mcp_risk" | "weak_evidence";
3
3
  export interface TraceInput {
4
4
  path: string;
5
5
  content: string;
package/docs/BENCHMARK.md CHANGED
@@ -20,6 +20,7 @@ This benchmark runs the public fixture pack that ships with the repository and p
20
20
  | Codex session resume and state failure | `fixtures/codex-session-state.md` | 59 | 3 | 0 | `codex_resource_leak`, `codex_session_state`, `weak_evidence` | pass |
21
21
  | Codex token burn and usage-drain loop | `fixtures/codex-token-burn.md` | 59 | 3 | 0 | `codex_resource_leak`, `codex_token_burn`, `weak_evidence` | pass |
22
22
  | Codex resource leak and runaway process | `fixtures/codex-resource-leak.md` | 75 | 2 | 0 | `codex_resource_leak`, `weak_evidence` | pass |
23
+ | Codex tool-call integrity and rollback failure | `fixtures/codex-tool-call-integrity.md` | 59 | 3 | 0 | `codex_resource_leak`, `codex_tool_call_integrity`, `weak_evidence` | pass |
23
24
  | Untrusted PR comment prompt injection | `fixtures/prompt-injection.md` | 50 | 3 | 1 | `premature_completion`, `prompt_injection`, `weak_evidence` | pass |
24
25
  | Conflicting agent instruction files | `fixtures/instruction-drift` | 84 | 1 | 0 | `ignored_instruction` | pass |
25
26
 
package/docs/CODEX_ISSUE_MAP.md CHANGED
@@ -18,6 +18,7 @@ npx trace-to-skill codex-report redacted-runs --output openai-codex-issue.md
18
18
  | --- | --- | --- | --- |
19
19
  | Token burn and usage drain | `tokens burning very fast`, large cached input totals, `write_stdin` empty polls, idle app usage, compaction tax, retry loops | `codex_token_burn` | `trace-to-skill codex-report ./runs` |
20
20
  | Resource leaks and runaway processes | high CPU/GPU/RAM, `Code Helper`, `Codex Helper Renderer`, orphaned `shell-snapshot`, `syspolicyd`, log floods, thinking animation GPU loops | `codex_resource_leak` | `trace-to-skill codex-report ./runs` |
21
+ | Tool-call integrity and rollback failures | `apply_patch` overwrites an existing `Add File` target, unmatched `tool_call_id`, `close_agent` hangs, failed revert/undo, unsafe diff application | `codex_tool_call_integrity` | `trace-to-skill codex-report ./runs` |
21
22
  | Quota mismatch | `/status` or usage page shows quota left, but runtime says `You've hit your usage limit`; account/workspace reset or cache confusion | `quota_mismatch` | `trace-to-skill codex-report ./runs` |
22
23
  | Sensitive file exclusion | `.env`, private keys, `.npmrc`, cloud credentials, local databases, or production secret manifests entered agent context | `sensitive_file_access` | `trace-to-skill codex-report ./runs` |
23
24
  | Context compaction failures | `Error running remote compact task`, `context_length_exceeded`, compaction loops, `responses/compact` stream disconnects | `context_compaction` | `trace-to-skill analyze ./runs` |
@@ -36,6 +37,7 @@ npx trace-to-skill codex-report redacted-runs --output openai-codex-issue.md
36
37
  - Include the smallest redacted trace that reproduces the failure.
37
38
  - Include before/after `/status` and usage dashboard state for quota or token-burn reports.
38
39
  - Include process names/PIDs, CPU/GPU/RSS samples, log-loop signatures, and whether killing exact PIDs or closing the app clears resource leaks.
40
+ - Include exact tool input/output, `tool_call_id` order, affected path state, and rollback evidence for tool-call integrity failures.
39
41
  - Include line-linked evidence rather than screenshots alone when logs are available.
40
42
  - Redact tokens, API keys, emails, local home paths, customer data, and hidden Unicode before posting publicly.
41
43
  - For sensitive-file reports, attach only redacted excerpts and the file path/class, not the original credential material.
@@ -44,6 +46,7 @@ npx trace-to-skill codex-report redacted-runs --output openai-codex-issue.md
44
46
 
45
47
  - Token burn and usage drain: https://github.com/openai/codex/issues/14593, https://github.com/openai/codex/issues/13733, https://github.com/openai/codex/issues/25420, https://github.com/openai/codex/issues/19585
46
48
  - Resource leaks and runaway processes: https://github.com/openai/codex/issues/16231, https://github.com/openai/codex/issues/11981, https://github.com/openai/codex/issues/16857, https://github.com/openai/codex/issues/25388
49
+ - Tool-call integrity and rollback failures: https://github.com/openai/codex/issues/25399, https://github.com/openai/codex/issues/25380, https://github.com/openai/codex/issues/25426, https://github.com/openai/codex/issues/7291
47
50
  - Session state and resume failures: https://github.com/openai/codex/issues/25430, https://github.com/openai/codex/issues/25390, https://github.com/openai/codex/issues/25394, https://github.com/openai/codex/issues/25407
48
51
  - MCP runtime failures: https://github.com/openai/codex/issues/16685, https://github.com/openai/codex/issues/18977, https://github.com/openai/codex/issues/24297, https://github.com/openai/codex/issues/23839
49
52
  - Sensitive file exclusion: https://github.com/openai/codex/issues/2847
package/docs/DISCOVERY.md CHANGED
@@ -80,7 +80,7 @@ npx trace-to-skill suggest ./runs --target agents-md
80
80
 
81
81
  ## Related Keywords
82
82
 
83
- Codex, OpenAI Codex, Codex issue report, OpenAI triage, Codex CLI, Codex sandbox, Windows sandbox, Codex auth, token_exchange_failed, Codex connectivity, stream disconnected, Codex remote control, Codex mobile, Waiting for desktop, Directory Unavailable, stale listener, Codex MCP runtime, MCP unsupported call, mcp__node_repl__js, MCP namespace serverName, MCP Transport closed, StdioServerTransport, Codex resume, Codex session state, rollout JSONL, thread_goals, state_5.sqlite, goals_1.sqlite, archived chats, Codex token burn, Codex usage drain, write_stdin polling, cached input tokens, compaction tax, background process polling, Codex resource leak, Codex performance, high CPU, high GPU, shell-snapshot, Code Helper Renderer, Codex quota, usage limit, rate limits, sensitive files, Codex privacy, .env, private keys, credential files, AGENTS.md, SKILL.md, Claude Code, Cursor, Copilot coding agent, Gemini CLI, MCP, Model Context Protocol, prompt injection, agent evals, AI code review, open-source maintainers, trace redaction, SARIF, GitHub Actions.
83
+ Codex, OpenAI Codex, Codex issue report, OpenAI triage, Codex CLI, Codex sandbox, Windows sandbox, Codex auth, token_exchange_failed, Codex connectivity, stream disconnected, Codex remote control, Codex mobile, Waiting for desktop, Directory Unavailable, stale listener, Codex MCP runtime, MCP unsupported call, mcp__node_repl__js, MCP namespace serverName, MCP Transport closed, StdioServerTransport, Codex resume, Codex session state, rollout JSONL, thread_goals, state_5.sqlite, goals_1.sqlite, archived chats, Codex token burn, Codex usage drain, write_stdin polling, cached input tokens, compaction tax, background process polling, Codex resource leak, Codex performance, high CPU, high GPU, shell-snapshot, Code Helper Renderer, Codex tool-call integrity, apply_patch, tool_call_id, close_agent, failed revert changes, patch safety, Codex quota, usage limit, rate limits, sensitive files, Codex privacy, .env, private keys, credential files, AGENTS.md, SKILL.md, Claude Code, Cursor, Copilot coding agent, Gemini CLI, MCP, Model Context Protocol, prompt injection, agent evals, AI code review, open-source maintainers, trace redaction, SARIF, GitHub Actions.
84
84
 
85
85
  ## Non-Goals
86
86
 
package/docs/FAILURE_TAXONOMY.md CHANGED
@@ -72,6 +72,14 @@ Common signals include high `Code Helper (Renderer)` or `Code Helper (Plugin)` C
72
72
 
73
73
  The fix is to capture app/extension/CLI version, OS, IDE, thread type, process names/PIDs, CPU/GPU/RSS samples over time, whether the process is orphaned, log-loop signatures, workspace Git-root state, animation/reduce-motion state, reproduction steps, and whether closing the panel/app, killing exact PIDs, `git init`, rollback, or restart clears the leak.
74
74
 
75
+ ## Codex Tool-Call Integrity
76
+
77
+ Codex patch, rollback, subagent, and protocol tool calls can fail in ways that threaten maintainer trust: `apply_patch` accepting `*** Add File` for an existing file, `tool_calls` messages missing matching tool responses, `close_agent` hanging after durable state says closed, or extension revert/undo failing after code was deleted.
78
+
79
+ Common signals include `apply_patch`, `*** Add File`, existing file overwrite, symlink target replacement, `assistant message with 'tool_calls' must be followed by tool messages`, missing `tool_call_id`, `close_agent` hanging forever, `agent thread limit reached`, `Failed to revert changes`, and deleted or truncated uncommitted code.
80
+
81
+ The fix is to capture exact tool input/output, app/CLI/extension version, OS/IDE, workspace git state, affected file path and whether it already existed or was a symlink, diff before/after, tool-call ordering, durable subagent/thread state, rollback attempts, and whether a clean repo reproduction fails the same way.
82
+
75
83
  ## Quota Mismatch
76
84
 
77
85
  Codex reports a usage-limit block even though another surface shows remaining quota, or quota state appears to be shared across accounts, consumed in parallel across 5h and weekly windows, or reset at an impossible time.
package/docs/RELEASE.md CHANGED
@@ -41,7 +41,7 @@ npx npm@11.16.0 trust github trace-to-skill \
41
41
  2. Run `npm run check`.
42
42
  3. Regenerate `docs/BENCHMARK.md` and `docs/SCORECARD.md` if benchmark fixtures changed.
43
43
  4. Commit and push to `main`.
44
- 5. Create a GitHub release whose tag matches the package version, such as `v0.1.40`.
44
+ 5. Create a GitHub release whose tag matches the package version, such as `v0.1.42`.
45
45
  6. Confirm the `Publish npm` workflow succeeds.
46
46
  7. Confirm `npm view trace-to-skill version dist-tags.latest --json` shows the new version.
47
47
 
package/docs/SCORECARD.md CHANGED
@@ -9,7 +9,7 @@ Status: **pass**
9
9
  | Failed doctor checks | 0 |
10
10
  | Critical findings | 0 |
11
11
  | Built-in benchmark | pass |
12
- | Benchmark cases | 16 |
12
+ | Benchmark cases | 17 |
13
13
 
14
14
  ## Doctor Summary
15
15
 
@@ -37,6 +37,7 @@ This benchmark runs the public fixture pack that ships with the repository and p
37
37
  | Codex session resume and state failure | `fixtures/codex-session-state.md` | 59 | 3 | 0 | `codex_resource_leak`, `codex_session_state`, `weak_evidence` | pass |
38
38
  | Codex token burn and usage-drain loop | `fixtures/codex-token-burn.md` | 59 | 3 | 0 | `codex_resource_leak`, `codex_token_burn`, `weak_evidence` | pass |
39
39
  | Codex resource leak and runaway process | `fixtures/codex-resource-leak.md` | 75 | 2 | 0 | `codex_resource_leak`, `weak_evidence` | pass |
40
+ | Codex tool-call integrity and rollback failure | `fixtures/codex-tool-call-integrity.md` | 59 | 3 | 0 | `codex_resource_leak`, `codex_tool_call_integrity`, `weak_evidence` | pass |
40
41
  | Untrusted PR comment prompt injection | `fixtures/prompt-injection.md` | 50 | 3 | 1 | `premature_completion`, `prompt_injection`, `weak_evidence` | pass |
41
42
  | Conflicting agent instruction files | `fixtures/instruction-drift` | 84 | 1 | 0 | `ignored_instruction` | pass |
42
43
 
package/docs/USE_CASES.md CHANGED
@@ -21,7 +21,7 @@ What it proves:
21
21
  Recommended CI surface:
22
22
 
23
23
  ```yaml
24
- - uses: grnbtqdbyx-create/trace-to-skill@v0.1.40
24
+ - uses: grnbtqdbyx-create/trace-to-skill@v0.1.42
25
25
  with:
26
26
  mode: all
27
27
  doctor-threshold: "85"
package/fixtures/codex-tool-call-integrity.md ADDED
@@ -0,0 +1,34 @@
1
+ # Codex Tool-Call Integrity Trace
2
+
3
+ User report:
4
+
5
+ Codex CLI 0.135.0 on Linux reproduced a tool-level patch safety bug:
6
+
7
+ ```text
8
+ apply_patch accepted *** Add File for an existing file and silently overwrote the original contents.
9
+ The target path already existed, but the result said "Success. Updated the following files: A existing.txt".
10
+ This is worse when the existing file is a symlink, because Add File can replace the linked target contents.
11
+ Expected behavior: Add File should fail when the target already exists.
12
+ ```
13
+
14
+ Second report:
15
+
16
+ ```text
17
+ Codex App returned invalid_request_error:
18
+ An assistant message with 'tool_calls' must be followed by tool messages responding to each 'tool_call_id'.
19
+ The task stopped after generating a presentation and did not produce a matching tool message for every tool_call_id.
20
+ ```
21
+
22
+ Third report:
23
+
24
+ ```text
25
+ multi_agent_v1.close_agent can hang forever after durable thread_spawn_edges status is already closed.
26
+ The child thread was interrupted, close_agent never returns, and later spawn_agent fails with agent thread limit reached because the registry slot is still counted.
27
+ ```
28
+
29
+ Fourth report:
30
+
31
+ ```text
32
+ VS Code Codex extension deleted uncommitted code and the revert changes button showed "Failed to revert changes".
33
+ The undo button stopped working, so the user had to manually restore code from the conversation history.
34
+ ```
package/llms.txt CHANGED
@@ -70,7 +70,7 @@ npx trace-to-skill init --comment --sarif
70
70
  ## GitHub Action
71
71
 
72
72
  ```yaml
73
- - uses: grnbtqdbyx-create/trace-to-skill@v0.1.40
73
+ - uses: grnbtqdbyx-create/trace-to-skill@v0.1.41
74
74
  with:
75
75
  mode: all
76
76
  doctor-threshold: "85"
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "trace-to-skill",
3
- "version": "0.1.40",
3
+ "version": "0.1.42",
4
4
  "description": "Turn failed AI coding-agent runs into reusable AGENTS.md rules, SKILL.md files, and eval evidence.",
5
5
  "type": "module",
6
6
  "main": "dist/src/index.js",
@@ -80,6 +80,8 @@
80
80
  "codex-usage",
81
81
  "codex-resource-leak",
82
82
  "codex-performance",
83
+ "codex-tool-calls",
84
+ "patch-safety",
83
85
  "quota-mismatch",
84
86
  "codex-rate-limits",
85
87
  "usage-limit",
package/schemas/analysis-result.schema.json CHANGED
@@ -76,6 +76,7 @@
76
76
  "codex_session_state",
77
77
  "codex_token_burn",
78
78
  "codex_resource_leak",
79
+ "codex_tool_call_integrity",
79
80
  "quota_mismatch",
80
81
  "mcp_risk",
81
82
  "weak_evidence"