fix: preserve accepted coverage through publication and recovery

.github/release-notes.md

@@ -1,37 +1,47 @@
-<!-- release-version: 0.1.27 -->
+<!-- release-version: 0.1.28 -->
 
 <!-- release-section: highlights:start -->
 ## Highlights
 
-- port source and test report checks to TypeScript ([#768](https://github.com/openai/codex-security/pull/768))
-- port custom validation to TypeScript ([#792](https://github.com/openai/codex-security/pull/792))
-- add Python-free Unix OS primitives ([#794](https://github.com/openai/codex-security/pull/794))
-- add Python-free Windows OS primitives ([#795](https://github.com/openai/codex-security/pull/795))
-- add Python-free musl native artifacts ([#796](https://github.com/openai/codex-security/pull/796))
-- bundle verified native runtime artifacts ([#797](https://github.com/openai/codex-security/pull/797))
-- preserve Windows filenames in native helpers ([#798](https://github.com/openai/codex-security/pull/798))
-- port security policy resolution to TypeScript ([#799](https://github.com/openai/codex-security/pull/799))
-- budget package installation and verification ([#834](https://github.com/openai/codex-security/pull/834))
-- open ready pull requests ([#833](https://github.com/openai/codex-security/pull/833))
-- draft SECURITY.md for owner review ([#536](https://github.com/openai/codex-security/pull/536))
-- resolve Windows Node to an absolute executable ([#788](https://github.com/openai/codex-security/pull/788))
-- shard automatic component planning for large repositories ([#845](https://github.com/openai/codex-security/pull/845))
-- import CSV and JSON findings as saved scans ([#850](https://github.com/openai/codex-security/pull/850))
-- add a feedback command ([#854](https://github.com/openai/codex-security/pull/854))
-- improve scan usage and cost reports ([#853](https://github.com/openai/codex-security/pull/853))
-- recover interrupted Deep Scans and bulk campaigns ([#835](https://github.com/openai/codex-security/pull/835))
-- reject owned plugin keys inside Codex profiles ([#861](https://github.com/openai/codex-security/pull/861))
-- include CommonJS and TypeScript module extensions in scan inventories ([#859](https://github.com/openai/codex-security/pull/859))
-- include workflow files in diff inventories ([#820](https://github.com/openai/codex-security/pull/820))
-- accept a UTF-8 byte order mark in imported findings JSON ([#856](https://github.com/openai/codex-security/pull/856))
-- authenticate deep workers with OpenAI API keys ([#870](https://github.com/openai/codex-security/pull/870))
-- drop canonical document size limits that do not exist ([#868](https://github.com/openai/codex-security/pull/868))
-- pin native Rust formatting edition ([#863](https://github.com/openai/codex-security/pull/863))
-- detect a Linear URL contradiction over plain HTTP ([#867](https://github.com/openai/codex-security/pull/867))
-- pipeline dedupe with configurable concurrency ([#852](https://github.com/openai/codex-security/pull/852))
-- disable reasoning summaries by default for Bedrock ([#869](https://github.com/openai/codex-security/pull/869))
-- reuse scan authentication for patch and validation ([#871](https://github.com/openai/codex-security/pull/871))
-- bump smol-toml from 1.6.1 to 1.7.1 in /sdk/typescript ([#873](https://github.com/openai/codex-security/pull/873))
+- use versioned conventional commit titles ([#879](https://github.com/openai/codex-security/pull/879))
+- share scan settings across the CLI and SDK ([#742](https://github.com/openai/codex-security/pull/742))
+- keep parameterized JUnit names unique ([#877](https://github.com/openai/codex-security/pull/877))
+- accept large saved post-scan prompts ([#876](https://github.com/openai/codex-security/pull/876))
+- make cost display optional ([#881](https://github.com/openai/codex-security/pull/881))
+- collect Desktop and worker session logs ([#872](https://github.com/openai/codex-security/pull/872))
+- skip unavailable Daybreak access advisories ([#878](https://github.com/openai/codex-security/pull/878))
+- align Codex 0.154.0 and dependency cooldowns ([#755](https://github.com/openai/codex-security/pull/755))
+- bump docker/setup-buildx-action from 4.2.0 to 4.3.0 ([#891](https://github.com/openai/codex-security/pull/891))
+- bump actions/attest-build-provenance from 4.1.1 to 4.2.2 ([#886](https://github.com/openai/codex-security/pull/886))
+- update setuptools requirement from \>=64.0 to \>=84.0.0 in /plugins/codex-security ([#889](https://github.com/openai/codex-security/pull/889))
+- bump SocketDev/action from 1.3.0 to 1.3.2 ([#884](https://github.com/openai/codex-security/pull/884))
+- bump ruff from 0.16.1 to 0.16.6 in /plugins/codex-security ([#887](https://github.com/openai/codex-security/pull/887))
+- bump typescript from 6.0.3 to 7.0.2 in /plugins/codex-security/mcp-app ([#894](https://github.com/openai/codex-security/pull/894))
+- bump pytest from 9.0.3 to 9.1.1 in /plugins/codex-security ([#885](https://github.com/openai/codex-security/pull/885))
+- bump typescript from 5.7.3 to 7.0.2 in /sdk/typescript ([#898](https://github.com/openai/codex-security/pull/898))
+- simplify fast-uri dependency and update Ajv resolver ([#895](https://github.com/openai/codex-security/pull/895))
+- bump @linear/sdk from 89.0.0 to 93.0.1 in /sdk/typescript ([#896](https://github.com/openai/codex-security/pull/896))
+- bump actions/checkout from 6.0.2 to 7.0.1 ([#890](https://github.com/openai/codex-security/pull/890))
+- bump actions/setup-node from 6.3.0 to 7.0.0 ([#888](https://github.com/openai/codex-security/pull/888))
+- bump @types/node from 22.19.17 to 26.4.1 in /sdk/typescript ([#897](https://github.com/openai/codex-security/pull/897))
+- bump @types/node from 25.9.1 to 26.4.1 in /plugins/codex-security/mcp-app ([#893](https://github.com/openai/codex-security/pull/893))
+- bump the third-party group across 3 directories with 19 updates ([#892](https://github.com/openai/codex-security/pull/892))
+- report patch failures and changed files ([#874](https://github.com/openai/codex-security/pull/874))
+- persist scan artifacts through MCP ([#862](https://github.com/openai/codex-security/pull/862))
+- advance scan progress when saving drafts ([#882](https://github.com/openai/codex-security/pull/882))
+- simplify scan runtime bookkeeping ([#903](https://github.com/openai/codex-security/pull/903))
+- upgrade json-schema-to-typescript to 16.0.0 ([#914](https://github.com/openai/codex-security/pull/914))
+- upgrade eval OpenCode SDK to 1.18.29 ([#911](https://github.com/openai/codex-security/pull/911))
+- upgrade Ink and use complete Escape input in TUI tests ([#913](https://github.com/openai/codex-security/pull/913))
+- upgrade pnpm setup and align the package-manager pin ([#910](https://github.com/openai/codex-security/pull/910))
+- upgrade actions/setup-python to 7.0.0 ([#909](https://github.com/openai/codex-security/pull/909))
+- upgrade Stryker with compatible mutation tooling ([#912](https://github.com/openai/codex-security/pull/912))
+- limit fix-finding to security vulnerabilities ([#923](https://github.com/openai/codex-security/pull/923))
+- accept text knowledge-base files with any extension ([#924](https://github.com/openai/codex-security/pull/924))
+- declare native release workflow permissions ([#925](https://github.com/openai/codex-security/pull/925))
+- report context-aware estimate ranges ([#926](https://github.com/openai/codex-security/pull/926))
+- update vulnerable image and archive dependencies ([#927](https://github.com/openai/codex-security/pull/927))
+- update Inquirer prompts and Node/Bun types ([#929](https://github.com/openai/codex-security/pull/929))
 <!-- release-section: highlights:end -->
 
 <!-- release-section: upgrades:start -->

.github/release-pr-state.json

@@ -1,9 +1,9 @@
 {
-  "baseVersion": "0.1.26",
-  "baseCommit": "2536d104deef9bca8ced84c6f6263b915418253b",
+  "baseVersion": "0.1.27",
+  "baseCommit": "c40d059935592adc1ae04119eb7ad5286d9de554",
   "sections": {
     "highlights": {
-      "generatedHash": "488ce0a2eadd5a3718a22b68227f42dbba6f3f57b1ad9259cc850c397318a977",
+      "generatedHash": "d0496c2cdec032d1ca5d28e8ae63b650918b93ebe458c76328734d47edc970d4",
       "humanOwned": false
     },
     "upgrades": {

plugins/codex-security/mcp-app/src/artifact-deep-reducer.ts

@@ -1,4 +1,4 @@
-import { join } from "node:path";
+import { dirname, join, relative, sep } from "node:path";
 import type { ZodType } from "zod/v4";
 import commonSchema from "../../schemas/definitions/artifact-common.schema.json";
 import reducerSchema from "../../schemas/tools/deep-reducer.schema.json";
@@ -20,7 +20,9 @@ import {
   type DeepScanArtifacts
 } from "./deep-scan/artifacts.js";
 import {
+  deepReductionForPersistence,
   parseDeepReduction,
+  projectDiscoveryCoverage,
   reconcileDeepReduction,
   type DeepReductionInput,
   type DeepReductionSources,
@@ -54,6 +56,18 @@ interface BoundReducer {
 /** Read the findings and scan context assigned to this reducer. */
 export async function getCodexSecurityDeepReducerInputs(
   context: ArtifactContext
+): Promise<DeepReductionSources> {
+  const inputs = await readDeepReductionSources(context);
+  const { sourceCoverage: _coverage, ...previous } = inputs.previous ?? {};
+  return {
+    discoveries: inputs.discoveries.map(({ workerId, result }) => ({ workerId, result })),
+    previous: inputs.previous === null ? null : previous as DeepReductionInput,
+  };
+}
+
+/** Capture host coverage alongside the reducer's immutable finding inputs. */
+export async function readDeepReductionSources(
+  context: ArtifactContext
 ): Promise<DeepReductionSources> {
   return withLogicalReducerErrors(context, async () => {
     const bound = bindDeepReducer(context);
@@ -73,8 +87,13 @@ export async function getCodexSecurityDeepReducerInputs(
           sourceFindingIds: [`${worker.id}:${index}`],
         },
       }));
-      const { coverage: _coverage, ...reduction } = result;
-      return { workerId: worker.id, result: reduction };
+      const { coverage, ...reduction } = result;
+      return {
+        workerId: worker.id,
+        ...(worker.attempt === undefined ? {} : { attempt: worker.attempt }),
+        coverage: projectDiscoveryCoverage(coverage, worker, relative(bound.artifacts.scanDir, dirname(worker.resultPath)).split(sep).join("/")),
+        result: reduction,
+      };
     }));
     const previous = await readPreviousReduction(bound);
     const scanId = bound.scanId ?? previous?.scanId ?? discoveries[0]?.result.scanId;
@@ -107,7 +126,7 @@ export async function recordCodexSecurityDeepReduction(
     const submitted = deepReductionInputSchema.parse(input);
     let reduction = parseDeepReduction(submitted);
     if (reduction.complete === false) throw new Error("Deep reduction is only a checkpoint, not a complete result.");
-    const inputs = await getCodexSecurityDeepReducerInputs(context);
+    const inputs = await readDeepReductionSources(context);
     const expectedScanId = bound.scanId
       ?? inputs.previous?.scanId
       ?? inputs.discoveries[0]?.result.scanId;
@@ -116,8 +135,9 @@ export async function recordCodexSecurityDeepReduction(
     }
     reduction = reconcileDeepReduction(reduction, inputs.discoveries, inputs.previous);
 
-    await saveScanDraftCheckpoint(context, reduction);
-    await writeJsonAtomic(bound.resultPath, reduction);
+    const persisted = deepReductionForPersistence(reduction, bound.state.persistSourceCoverage);
+    await saveScanDraftCheckpoint(context, persisted);
+    await writeJsonAtomic(bound.resultPath, persisted);
     return {
       findingCount: reduction.findings.length,
       consumedWorkerIds: bound.state.claimedWorkers.map((worker) => worker.id)

plugins/codex-security/mcp-app/src/artifact-io.ts

@@ -5,12 +5,14 @@ import { dirname, isAbsolute, join, resolve, sep } from "node:path";
 export interface DeepReducerWorkerContext {
   id: string;
   resultPath: string;
+  attempt?: number;
 }
 
 export interface DeepReducerContext {
   scanRoot: string;
   claimedWorkers: DeepReducerWorkerContext[];
   previousReducerResultPath?: string;
+  persistSourceCoverage?: boolean;
 }
 
 /**

plugins/codex-security/mcp-app/src/artifact-scan-draft.ts

@@ -1,6 +1,6 @@
 import { createHash, randomUUID } from "node:crypto";
 import { promises as fs } from "node:fs";
-import { dirname, join, sep } from "node:path";
+import { basename, dirname, join, sep } from "node:path";
 import type * as z from "zod/v4";
 import commonSchema from "../../schemas/definitions/artifact-common.schema.json";
 import scanDraftDocument from "../../schemas/tools/scan-draft.schema.json";
@@ -596,6 +596,7 @@ async function readArchivedWorkerCheckpoints(
   }
 
   const archived: ScanDraftInput[] = [];
+  const archivePrefix = `artifacts/deep_discovery/workers/${basename(workerRoot)}/attempts/`;
   const attempts = (await fs.readdir(canonicalAttemptsRoot, { withFileTypes: true }))
     .filter((entry) => entry.isDirectory() && !entry.isSymbolicLink())
     .sort((left, right) => archivedAttemptNumber(right.name) - archivedAttemptNumber(left.name)
@@ -704,8 +705,18 @@ async function readArchivedWorkerCheckpoints(
     drafts.sort((left, right) => right.modifiedMs - left.modifiedMs
       || Number(right.result) - Number(left.result)
       || right.name.localeCompare(left.name));
-    if (checkpointHead !== undefined) archived.push(checkpointHead);
-    archived.push(...drafts.map((draft) => draft.input));
+    const inputs = [...(checkpointHead ? [checkpointHead] : []), ...drafts.map((draft) => draft.input)];
+    for (const input of inputs) {
+      // The archive moved the receipts with this attempt. Rebase only the
+      // retained projection; the original checkpoint bytes remain unchanged.
+      for (const surface of input.coverage.surfaces as JsonObject[]) {
+        if (!Array.isArray(surface.receiptRefs)) continue;
+        surface.receiptRefs = (surface.receiptRefs as string[]).map((ref) => (
+          ref.startsWith(archivePrefix) ? ref : `${archivePrefix}${attempt.name}/${ref}`
+        ));
+      }
+      archived.push(input);
+    }
   }
   return archived;
 }