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PaperClipAI/packages/paperclip-runner/package.json
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DottaandPaperclip 3b550c80fa fix(codex): correct startup trust, history reads, and resume usage (#13110) 
## Thinking Path

> - Paperclip runs Codex locally and in remote sandboxes.
> - The runner must preserve startup configuration and session identity.
> - Missing project trust can disable repository configuration.
> - Full-history requests use deprecated provider fields.
> - Resume usage describes old work and must not become new run usage.
> - This change corrects startup trust, state reads, and usage
classification.

## Linked Issues or Issue Description

**What happened?**

Normal Codex runs could show repository-trust and history-deprecation
warnings.
Resume could report the preceding turn's token snapshot as a late-turn
warning.
The historical last-usage value could also be attributed to the new run.

**Expected behavior**

Trust the server-selected startup root in isolated configuration. Read
lightweight
provider state and paginated evidence. Use historical cumulative usage
as a
baseline without a new charge or user-facing warning.

**Steps to reproduce**

1. Start a native Codex task in a selected repository.
2. Finish the turn and resume the provider thread.
3. Inspect provider notices, history requests, and per-run usage.
4. Repeat startup and cold resume inside a Daytona sandbox.

**Paperclip version or commit**

Codex CLI 0.153.4 is the pinned runtime and reproduced baseline.
Replayed onto master at 6abeb6733. Related authority work: Refs #13092.
This PR retains its startup cleanup and protocol-integrity checks.

**Deployment mode**

Local source checkout and disposable Daytona sandbox.

## What Changed

- Classify the exact historical resume usage event before the generic
stale-turn warning.
- Persist cumulative usage baselines across recovery of the same run.
- Use excludeTurns on resume and lightweight thread reads.
- Page turn metadata and selected turn items with cursor and identity
validation.
- Reject unsupported or incomplete history instead of guessing that
execution is idle.
- Trust the startup execution root on its host, including Git worktree
trust keys.
- Start Codex in that root and retain the selected sandbox profile on
later turns.
- Keep unrelated isolated configuration and Codex's separate hook trust
policy.
- Add Rust, TypeScript, accounting, native integration, and local
run-log documentation.

## Verification

- Codex and native-transport TypeScript: 333 passed before PR replay.
- Adjacent OpenCode/ACPX driver and accounting tests: 49 passed.
- Rust library, serialized: 226 passed. Native Codex integration: 72
passed, 1 ignored, plus two pagination regressions.
- Repository typecheck and build passed. All repository test groups have
passing coverage after fixture and resource retests; the initial
monolithic command was not clean.
- Fresh real Codex native browser tasks returned correct answers without
the three targeted notices. Answers persisted after refresh and restart.
- Real same-thread TypeScript driver tests passed locally and in
Daytona, including cold resume, configuration, skills, and an approved
harmless hook.
- Local usage summed to 64,607 tokens. Daytona usage summed to 42,737
tokens. Each sum matched its final session total exactly.
- See doc/plans/2026-09-09-codex-integration-acceptance.md for the scope
and limits of the live tests.
- After replay onto current master and review fixes: 334 Codex, backend,
and live-session tests passed, including checkpoint serialization and
real-runner process restart. TypeScript checks passed.
- The native Codex integration run passed 83 tests; the large lineage
test passed separately with the release runner (its debug build exceeded
the test deadline).
- All GitHub checks passed on the final PR head. Greptile is 5/5 with no
unresolved review threads. CI regenerates the lockfile for the added
TOML dependency, per repository policy.
- The first server shard hit a timing-dependent duplicate-key failure in
the unchanged artifact-document concurrency test. Its focused 11-test
suite passed locally. One CI retry on the same head passed all 103 files
and 1,405 tests (2 skipped): [retry
result](https://github.com/paperclipai/paperclip/actions/runs/34398832930/job/102631274667).

## Risks

- Trust applies only to the server-selected startup root and isolated
configuration. Sandbox and tool permissions remain authoritative.
- Codex still requires approval of individual hook hashes. This change
does not bypass that policy.
- Providers without the required history APIs fail explicitly.
- Daytona acceptance used the production TypeScript driver. Remote
Paperclip UI and remote Rust execution were not tested.
- No new public API, database state, recovery policy, or UI control is
included.

## Model Used

OpenAI Codex, GPT-6 (`gpt-6-astra`). Used for reasoning, code edits,
tool use,
and test execution. The exact context-window limit is not exposed in
this
session. Real-provider acceptance used Codex CLI 0.153.4 with
`gpt-5.6-sol`.

## Checklist

- [x] I have included a thinking path that traces from project context
to this change
- [x] I have specified the model used (with version and capability
details)
- [x] I have checked ROADMAP.md and confirmed this PR does not duplicate
planned core work
- [x] I have searched GitHub for duplicate or related PRs and linked
them above
- [x] I have either (a) linked existing issues with `Fixes: #` / `Closes
#` OR (b) described the issue in-PR following the relevant issue
template
- [x] I have not referenced internal/instance-local Paperclip issues or
links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip`
URLs)
- [x] My branch name describes the change (e.g. `docs/...`, `fix/...`)
and contains no internal Paperclip ticket id or instance-derived details
- [x] I have run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] All Paperclip CI gates are green
- [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups
- [x] I will address all Greptile and reviewer comments before
requesting merge

---------

Co-authored-by: Paperclip <noreply@paperclip.ing>
2026-09-09 15:35:18 -05:00

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{
"name": "@paperclipai/paperclip-runner",
"version": "0.0.0",
"private": true,
"license": "MIT",
"engines": {
"node": ">=24.11.0"
},
"type": "module",
"bin": {
"paperclip-runner-eval-session": "./dist/cli/eval-session.js",
"paperclip-runner-codex-proxy": "./dist/cli/codex-app-server-unix-proxy.js",
"paperclip-runner-opencode-proxy": "./dist/cli/opencode-app-server-proxy.js",
"paperclip-runner-acpx-sidecar": "./dist/cli/acpx-runtime-sidecar.js"
},
"exports": {
".": {
"types": "./dist/index.d.ts",
"import": "./dist/index.js"
},
"./testing": {
"types": "./dist/testing.d.ts",
"import": "./dist/testing.js"
},
"./evals": {
"types": "./dist/evals/index.d.ts",
"import": "./dist/evals/index.js"
},
"./live": {
"types": "./dist/live/index.d.ts",
"import": "./dist/live/index.js"
},
"./devtools": {
"types": "./dist/devtools/index.d.ts",
"import": "./dist/devtools/index.js"
},
"./browser": {
"types": "./dist/browser/index.d.ts",
"import": "./dist/browser/index.js"
},
"./react": {
"types": "./dist/react/index.d.ts",
"import": "./dist/react/index.js"
},
"./standalone": {
"types": "./dist/standalone/index.d.ts",
"import": "./dist/standalone/index.js"
},
"./styles.css": "./styles.css"
},
"files": [
"dist",
"dist-issue-thread",
"protocol",
"styles.css",
"README.md"
],
"sideEffects": false,
"scripts": {
"build": "pnpm run check:protocol-manifest && pnpm run build:typescript && pnpm run check:capability-contract && pnpm run check:capability-inventory && pnpm run check:protocol-coverage && pnpm run check:semantic-contracts && pnpm run check:runner-workflow-traceability && pnpm run build:binary && node scripts/generate-replay-goldens.mjs --check && node scripts/generate-semantic-action-catalog.mjs --check",
"build:typescript": "pnpm run ensure:eval-build-deps && pnpm run check:protocol-types && node ./node_modules/typescript/bin/tsc --version && node ./node_modules/typescript/bin/tsc -p tsconfig.json && node ./node_modules/typescript/bin/tsc -p tsconfig.surfaces.json && node scripts/build-verified-provider-entrypoints.mjs",
"build:rust": "cargo build --manifest-path runner/Cargo.toml --locked --workspace --bins",
"build:binary": "cargo build --release --manifest-path runner/Cargo.toml --locked -p paperclip-runner-core --bin paperclip-runnerd && node scripts/stage-runner-binary.mjs",
"build:provider-pack": "pnpm run build:typescript && node scripts/build-provider-pack.mjs",
"build:runner-binaries": "cargo build --manifest-path runner/Cargo.toml --locked --workspace --bins",
"build:browser": "vite build --config vite.config.ts",
"build:sdk": "vite build --config vite.sdk.config.ts",
"build:standalone": "vite build --config vite.standalone.config.ts",
"build:scenarios": "vite build --config vite.scenarios.config.ts && node scripts/check-capability-csp-bundle.mjs",
"build:issue-thread": "vite build --config vite.issue-thread.config.ts",
"typecheck": "pnpm run typecheck:typescript && pnpm run typecheck:rust",
"typecheck:typescript": "pnpm run ensure:eval-build-deps && node --check scripts/protocol-contract.mjs && node --check scripts/generate-protocol-manifest.mjs && node --check scripts/generate-protocol-schema-module.mjs && node --check scripts/generate-acpx-sidecar-contract.mjs && node --check scripts/generate-replay-goldens.mjs && node --check scripts/generate-semantic-action-catalog.mjs && pnpm run check:protocol-types && node ./node_modules/typescript/bin/tsc --version && node ./node_modules/typescript/bin/tsc -p tsconfig.json --noEmit && node ./node_modules/typescript/bin/tsc -p tsconfig.surfaces.json --noEmit",
"typecheck:rust": "cargo fmt --manifest-path runner/Cargo.toml --all -- --check && cargo check --manifest-path runner/Cargo.toml --locked --workspace",
"typecheck:browser": "tsc -p tsconfig.browser.json --noEmit",
"test": "pnpm run test:typescript && pnpm run test:rust",
"test:typescript": "pnpm run ensure:eval-build-deps && pnpm run build:rust && node --test test/protocol-contract.test.mjs test/acpx-sidecar-contract.test.mjs test/acpx-codex-package-contract.test.mjs scripts/aws-agentcore-provisioning.test.mjs scripts/build-verified-provider-entrypoints.test.mjs scripts/local-provider-smoke-environment.test.mjs scripts/materialize-opencode-binary.test.mjs && vitest run",
"test:rust": "cargo test --release --manifest-path runner/Cargo.toml --locked --workspace",
"test:codex": "cargo test --manifest-path runner/Cargo.toml --locked -p paperclip-runner-core --test codex_provider",
"test:durable": "cargo test --manifest-path runner/Cargo.toml --locked -p paperclip-runner-core durable::",
"test:browser": "pnpm run build:typescript && pnpm run build:runner-binaries && pnpm run build:browser && playwright test --config devtools/browser/playwright.config.ts",
"test:sdk": "vitest run src/browser/client.test.ts src/browser/transcript-model.test.ts src/react/public-contract.test.tsx",
"test:scenarios": "vitest run src/scenarios src/live src/semantic-tools/semantic-tools.test.ts src/mock-core/capability-mock-control-plane-adapter.test.ts src/issue-thread devtools/issue-thread/src examples/scenario-explorer",
"test:browser:sdk": "pnpm run build:typescript && playwright test --config examples/playwright.config.ts",
"test:browser:scenarios": "playwright test --config examples/playwright.scenarios.config.ts && pnpm run test:browser:issue-thread",
"test:browser:issue-thread": "pnpm run build:typescript && pnpm run build:issue-thread && playwright test --config devtools/issue-thread/playwright.config.ts",
"record:sdk:codex": "pnpm run build:typescript && playwright test --config examples/playwright.real.config.ts",
"generate:protocol-manifest": "node scripts/generate-protocol-manifest.mjs",
"check:protocol-manifest": "node scripts/generate-protocol-manifest.mjs --check",
"generate:protocol-types": "node scripts/generate-protocol-schema-module.mjs && node scripts/generate-acpx-sidecar-contract.mjs",
"check:protocol-types": "node scripts/generate-protocol-schema-module.mjs --check && node scripts/generate-acpx-sidecar-contract.mjs --check",
"generate:capability-contract": "node scripts/generate-capability-contract.mjs",
"check:capability-contract": "node scripts/generate-capability-contract.mjs --check",
"generate:semantic-contracts": "pnpm run build:typescript && node scripts/generate-semantic-contracts.mjs",
"check:semantic-contracts": "pnpm run build:typescript && node scripts/generate-semantic-contracts.mjs --check",
"generate:semantic-action-catalog": "pnpm run build:typescript && node scripts/generate-semantic-action-catalog.mjs",
"check:semantic-action-catalog": "pnpm run build:typescript && node scripts/generate-semantic-action-catalog.mjs --check",
"check:protocol": "pnpm run typecheck:typescript && pnpm run check:protocol-manifest && pnpm run test:typescript && pnpm run check:replay-goldens",
"check:runner": "pnpm run typecheck:rust && pnpm run test:rust && pnpm run check:conformance-parity && pnpm run check:replay-parity",
"check:all": "pnpm run check:eval-kernel && pnpm run check:protocol && pnpm run check:runner && pnpm run check:api-authority",
"check:api-authority": "node scripts/check-api-authority.mjs",
"generate:replay-goldens": "pnpm run build:typescript && node scripts/generate-replay-goldens.mjs",
"check:replay-goldens": "pnpm run build:typescript && node scripts/generate-replay-goldens.mjs --check",
"check:browser-tokens": "node scripts/check-browser-tokens.mjs",
"check:forbidden-imports": "node scripts/check-forbidden-imports.mjs",
"check:tracked-imports": "node scripts/check-tracked-imports.mjs",
"check:numbered-milestones": "node scripts/check-numbered-milestones.mjs",
"check:package-boundaries": "node scripts/check-package-boundaries.mjs",
"check:clean-consumers": "node scripts/check-clean-consumers.mjs",
"check:eval-kernel": "pnpm --filter @paperclipai/paperclip-eval-kernel test",
"ensure:eval-build-deps": "pnpm --filter @paperclipai/paperclip-eval-kernel build",
"generate:capability-inventory": "node scripts/generate-capability-inventory.mjs",
"generate:protocol-coverage": "pnpm run build:typescript && node scripts/generate-protocol-coverage.mjs",
"check:protocol-coverage": "node scripts/generate-protocol-coverage.mjs --check",
"check:capability-inventory": "node scripts/check-capability-inventory.mjs",
"test:capability-inventory": "node scripts/check-capability-inventory.test.mjs",
"test:capability-evals": "vitest run src/conformance/capability-eval-suite.test.ts",
"test:eval-slice": "pnpm run ensure:eval-build-deps && vitest run src/eval",
"test:runner-workflow-evals": "pnpm run ensure:eval-build-deps && node --test scripts/render-runner-workflow-evalbook.test.mjs && vitest run src/eval/workflow-evals.test.ts src/eval/live-workflow-executor.test.ts",
"test:runner-protocol-eval-publish": "node --test scripts/runner-protocol-eval-campaign.test.mjs scripts/publish-runner-protocol-eval-history.test.mjs scripts/runner-protocol-eval-metrics.test.mjs scripts/runner-protocol-eval-workflow-security.test.mjs scripts/public-eval-chat.test.mjs",
"check:runner-workflow-traceability": "pnpm run build:typescript && node scripts/check-runner-workflow-traceability.mjs",
"report:capability-evals": "pnpm run build:typescript && node scripts/run-capability-eval-suite.mjs",
"report:capability-live-evals": "pnpm run build:typescript && cargo build --manifest-path runner/Cargo.toml --locked -p paperclip-runner-core --bin paperclip-runnerd && node scripts/run-capability-live-eval-matrix.mjs",
"report:runner-workflow-evals": "pnpm run build:typescript && node scripts/run-runner-workflow-evals.mjs",
"report:runner-live-evals": "pnpm run build:typescript && pnpm run build:runner-binaries && node scripts/run-runner-live-eval-schedule.mjs --mode nightly --execute",
"report:runner-protocol-eval:catalog": "node scripts/runner-protocol-eval-campaign.mjs catalog",
"report:runner-protocol-eval:publish": "node scripts/publish-runner-protocol-eval-history.mjs",
"report:runner-chaos-evals": "pnpm run build:typescript && node scripts/run-runner-live-eval-schedule.mjs --mode chaos",
"check:conformance-parity": "cargo test --manifest-path runner/Cargo.toml --locked -p paperclip-runner-core runs_the_mock_core_path_with_stable_output",
"check:replay-parity": "cargo test --manifest-path runner/Cargo.toml --locked -p paperclip-runner-core replay_fixture_parity",
"docs:validate": "node scripts/validate-doc-links.mjs",
"trace:conformance": "pnpm run trace:conformance:rust",
"trace:conformance:rust": "cargo run --quiet --manifest-path runner/Cargo.toml --locked -p paperclip-runner-core --bin conformance-tracer",
"trace:conformance:typescript": "pnpm run build:typescript && node dist/tracer/conformance.js",
"replay:fixture": "pnpm run build:typescript && node dist/cli/replay.js",
"trace:local-runner": "pnpm run build:typescript && pnpm run build:runner-binaries && node dist/cli/local-runner.js",
"trace:codex": "pnpm run build:typescript && node dist/cli/codex.js",
"trace:standalone": "pnpm run build:typescript && node dist/cli/paperclip-adapter.js",
"trace:live-runner": "pnpm run build:typescript && cargo build --manifest-path runner/Cargo.toml --locked -p paperclip-runner-core --bin paperclip-runnerd && node dist/cli/live-runner.js",
"demo:standalone": "pnpm run build:typescript && vite --config vite.standalone.config.ts --host 127.0.0.1 --port 4182",
"demo:scenarios": "pnpm run build:typescript && vite --config vite.scenarios.config.ts --host 127.0.0.1 --port 4183",
"console:issue-thread": "pnpm run build:typescript && vite --config vite.issue-thread.config.ts --host 127.0.0.1 --port 4184",
"aws-agentcore:provision": "bash scripts/aws-agentcore.sh provision",
"aws-agentcore:probe": "bash scripts/aws-agentcore.sh probe",
"aws-agentcore:lab": "bash scripts/aws-agentcore.sh lab",
"aws-agentcore:destroy": "bash scripts/aws-agentcore.sh destroy",
"test:aws-agentcore-provisioning": "node --test scripts/aws-agentcore-provisioning.test.mjs",
"smoke:capability:aws-agentcore": "pnpm run build:typescript && cargo build --manifest-path runner/Cargo.toml --locked -p paperclip-runner-core --bin paperclip-runnerd && node scripts/capability-aws-agentcore-smoke.mjs",
"demo:live-console": "pnpm run build:typescript && node scripts/live-console-demo-server.mjs",
"smoke:capability:ui": "pnpm run build:typescript && cargo build --manifest-path runner/Cargo.toml --locked -p paperclip-runner-core --bin paperclip-runnerd && node scripts/capability-issue-thread-smoke.mjs",
"smoke:capability:cleanroom": "pnpm run build:typescript && cargo build --manifest-path runner/Cargo.toml --locked -p paperclip-runner-core --bin paperclip-runnerd && node scripts/capability-clean-room-smoke.mjs",
"smoke:local-provider": "node scripts/run-local-provider-smoke.mjs",
"console:live-console": "pnpm run build:typescript && vite --config vite.config.ts --host 127.0.0.1 --port 4180",
"console:sdk": "pnpm run build:typescript && vite --config vite.sdk.config.ts --host 127.0.0.1 --port 4181",
"browser:dev": "pnpm run build:typescript && pnpm run build:runner-binaries && vite --config vite.config.ts",
"browser:preview": "vite preview --config vite.config.ts",
"verify": "pnpm run build && pnpm run typecheck && pnpm run check:replay-goldens && pnpm run test && pnpm run test:sdk && pnpm run test:scenarios && pnpm run check:browser-tokens && pnpm run test:browser && pnpm run test:browser:sdk && pnpm run test:browser:scenarios && pnpm run check:forbidden-imports && pnpm run check:tracked-imports && pnpm run check:numbered-milestones && pnpm run check:package-boundaries && pnpm run check:clean-consumers && pnpm run docs:validate && pnpm run check:conformance-parity && pnpm run check:replay-parity && pnpm run trace:conformance && pnpm run replay:fixture && pnpm run trace:local-runner -- --quiet",
"verify:rootless": "bash scripts/verify-rootless-linux.sh"
},
"dependencies": {
"@agentclientprotocol/claude-agent-acp": "0.70.0",
"@agentclientprotocol/codex-acp": "1.6.2",
"@openai/codex": "0.153.4",
"acpx": "0.13.1",
"ajv": "^8.20.0",
"json-schema-to-ts": "^3.1.1",
"opencode-ai": "1.18.29",
"react-markdown": "^10.1.0",
"remark-gfm": "^4.0.1",
"smol-toml": "^1.4.2"
},
"peerDependencies": {
"react": ">=18",
"react-dom": ">=18"
},
"peerDependenciesMeta": {
"react": {
"optional": true
},
"react-dom": {
"optional": true
}
},
"devDependencies": {
"@paperclipai/paperclip-eval-kernel": "workspace:*",
"@playwright/test": "^1.61.1",
"@types/node": "^24.0.0",
"@types/react": "^19.2.17",
"@types/react-dom": "^19.2.5",
"@vitejs/plugin-react": "^4.7.0",
"axe-core": "^4.12.1",
"react": "^19.2.7",
"react-dom": "^19.2.7",
"tsx": "^4.23.12",
"typescript": "^7.0.2",
"vite": "^6.1.0",
"vitest": "^4.1.11"
}
}
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