Expose deep scan controls

README.md

@@ -16,6 +16,7 @@ npm install @openai/codex-security
 npx @openai/codex-security login
 npx @openai/codex-security scan .
 npx @openai/codex-security scan . --model gpt-5.6-terra --effort high
+npx @openai/codex-security scan . --mode deep --workers 2 --subagents 0 --stop-after-no-new 3 --max-discovery-runs 10
 ```
 
 For CI, set `OPENAI_API_KEY` or `CODEX_API_KEY` instead of signing in. Environment API keys are
@@ -58,6 +59,13 @@ import { CodexSecurity } from "@openai/codex-security";
 
 const security = new CodexSecurity();
 const result = await security.run(".");
+await security.run(".", {
+  mode: "deep",
+  workers: 2,
+  subagents: 0,
+  stopAfterNoNew: 3,
+  maxDiscoveryRuns: 10,
+});
 
 console.log(result.reportPath);
 await security.close();

sdk/typescript/README.md

@@ -183,6 +183,7 @@ npx @openai/codex-security scan /path/to/repository --output-dir /path/outside/r
 npx @openai/codex-security scan /path/to/repository --dry-run
 npx @openai/codex-security scan /path/to/repository --fail-on-severity high
 npx @openai/codex-security scan /path/to/repository --max-cost 5
+npx @openai/codex-security scan /path/to/repository --mode deep --workers 2 --subagents 0 --stop-after-no-new 3 --max-discovery-runs 10
 npx @openai/codex-security install-hook
 npx @openai/codex-security bulk-scan
 npx @openai/codex-security bulk-scan --model gpt-5.6-terra --effort high
@@ -224,6 +225,37 @@ to
 Repeat `--knowledge-base PATH` for multiple files or directories. Directories are
 searched recursively for Markdown, text, PDF, and Word (`.docx`) files.
 
+### Configure deep scans
+
+For `scan --mode deep`, `--workers` limits concurrent discovery workers,
+`--subagents` controls each worker's subagents, `--stop-after-no-new` stops after
+that many runs find no new issues, and `--max-discovery-runs` limits total runs.
+These options are also available on SDK scans:
+
+```ts
+await security.run("/path/to/repository", {
+  mode: "deep",
+  workers: 2,
+  subagents: 0,
+  stopAfterNoNew: 3,
+  maxDiscoveryRuns: 10,
+});
+```
+
+Set defaults in `~/.codex/codex-security/config.toml`, or under `$CODEX_HOME`
+when it is configured. Explicit CLI and SDK settings override these defaults:
+
+```toml
+[deep_scan]
+workers = 2
+subagents = 0
+stop_after_no_new = 3
+max_discovery_runs = 10
+```
+
+`scan --workers` controls discovery workers within one deep scan;
+`bulk-scan --workers` controls how many repositories are scanned concurrently.
+
 On macOS/Linux, an existing output directory must be private to the current
 user (`chmod 700`).
 

sdk/typescript/_bundled_plugin/scripts/deep_scan_workbench.py

@@ -531,6 +531,30 @@ def begin_deep_scan_for_scan(
     args: argparse.Namespace,
 ) -> dict[str, Any]:
     scan_id = require_uuid(scan_id, "scan-id")
+    candidate = require_scan(connection, scan_id)
+    workspace = require_workspace(connection, candidate["workspace_id"])
+    if (
+        candidate["mode"] == "deep"
+        and candidate["status"] == "running"
+        and candidate["recipe_json"] is not None
+        and candidate["handoff_status"] == "delivered"
+        and candidate["deep_scan_owner_thread_id"] is None
+        and workspace["thread_id"] is None
+    ):
+        timestamp = now()
+        with connection:
+            claimed_workspace = connection.execute(
+                "UPDATE workspaces SET thread_id = ?, updated_at = ? "
+                "WHERE id = ? AND thread_id IS NULL",
+                (thread_id, timestamp, workspace["id"]),
+            )
+            claimed_scan = connection.execute(
+                "UPDATE scans SET deep_scan_owner_thread_id = ?, updated_at = ? "
+                "WHERE id = ? AND deep_scan_owner_thread_id IS NULL",
+                (thread_id, timestamp, scan_id),
+            )
+            if claimed_workspace.rowcount != 1 or claimed_scan.rowcount != 1:
+                raise SystemExit("A scan can only be orchestrated from its owning Codex thread.")
     scan, _ = require_owned_scan(connection, scan_id, thread_id)
     require_current_continuation(
         scan,

sdk/typescript/src/api.ts

@@ -1,10 +1,23 @@
 /// <reference lib="esnext.disposable" preserve="true" />
 
-import { chmod, lstat, mkdir, realpath, rm, writeFile } from "node:fs/promises";
+import {
+  chmod,
+  lstat,
+  mkdir,
+  readFile,
+  realpath,
+  rm,
+  writeFile,
+} from "node:fs/promises";
 import { randomUUID } from "node:crypto";
 import { homedir, tmpdir } from "node:os";
 import { basename, dirname, isAbsolute, join, relative, sep } from "node:path";
 import { Codex, type CodexOptions } from "@openai/codex-sdk";
+import {
+  parse as parseToml,
+  stringify as stringifyToml,
+  type TomlTable,
+} from "smol-toml";
 import {
   accountStatus,
   CodexLoginHandle,
@@ -119,7 +132,14 @@ interface PreparedRuntime {
   effectiveConfig?: JsonObject;
 }
 
-export interface ScanOptions {
+export interface DeepScanOptions {
+  workers?: number;
+  subagents?: number;
+  stopAfterNoNew?: number;
+  maxDiscoveryRuns?: number;
+}
+
+export interface ScanOptions extends DeepScanOptions {
   auth?: ScanAuthMode;
   target?: ScanTarget;
   mode?: ScanMode;
@@ -174,7 +194,7 @@ type ScanObserverName =
   | "onWorkerStatus"
   | "onWarning";
 
-export interface ScanPreflight {
+export interface ScanPreflight extends DeepScanOptions {
   repository: string;
   target: NormalizedTarget;
   mode: ScanMode;
@@ -219,6 +239,12 @@ const DEFAULT_DEPENDENCIES: ClientDependencies = {
 };
 
 const SCAN_PERMISSION_PROFILE = "codex_security_scan";
+const DEEP_SCAN_SETTINGS = [
+  ["workers", "workers", 1],
+  ["subagents", "subagents", 0],
+  ["stopAfterNoNew", "stop_after_no_new", 1],
+  ["maxDiscoveryRuns", "max_discovery_runs", 1],
+] as const;
 
 export class CodexSecurity {
   public readonly config: Readonly<CodexSecurityConfig>;
@@ -282,6 +308,7 @@ export class CodexSecurity {
       repository: inputs.repository,
       target: inputs.target,
       mode: inputs.mode,
+      ...deepScanOptions(options),
       ...(options.knowledgeBasePaths?.length
         ? { knowledgeBasePaths: options.knowledgeBasePaths }
         : {}),
@@ -409,6 +436,14 @@ export class CodexSecurity {
       }
       const runtimeHome = await realpath(runtime.codexHome);
       requireOutputOutsideRepository(protectedRoot, runtimeHome, "runtime");
+      if (mode === "deep") {
+        await prepareDeepScanConfig(
+          runtimeHome,
+          this.#dependencies.environment,
+          options,
+          signal,
+        );
+      }
       if (
         options.expectedPluginVersion !== undefined &&
         runtime.plugin.version !== options.expectedPluginVersion
@@ -579,6 +614,7 @@ export class CodexSecurity {
         options.failureSeverity,
         knowledgeBase?.sources,
         options.maxCostUsd,
+        deepScanOptions(options),
       );
       const workbenchOptions: WorkbenchCommandOptions = {
         python,
@@ -1200,6 +1236,7 @@ export class CodexSecurity {
     options: ScanOptions,
     signal?: AbortSignal,
   ): Promise<LocalScanInputs> {
+    deepScanOptions(options);
     if (
       options.maxCostUsd !== undefined &&
       (!Number.isFinite(options.maxCostUsd) || options.maxCostUsd <= 0)
@@ -1340,6 +1377,71 @@ export class CodexSecurity {
   }
 }
 
+function deepScanOptions(options: ScanOptions): DeepScanOptions {
+  const selected: DeepScanOptions = {};
+  for (const [name, , minimum] of DEEP_SCAN_SETTINGS) {
+    const value = options[name];
+    if (value === undefined) continue;
+    if ((options.mode ?? "standard") !== "deep") {
+      throw new CodexSecurityError("Deep scan settings require deep mode.");
+    }
+    if (!Number.isSafeInteger(value) || value < minimum) {
+      throw new CodexSecurityError(
+        `Deep scan ${name} must be ${minimum === 0 ? "a non-negative" : "a positive"} integer.`,
+      );
+    }
+    selected[name] = value;
+  }
+  return selected;
+}
+
+async function prepareDeepScanConfig(
+  codexHome: string,
+  environment: ProcessEnvironment,
+  options: DeepScanOptions,
+  signal: AbortSignal,
+): Promise<void> {
+  const ambientHome =
+    environmentValue(environment, "CODEX_HOME") ?? join(homedir(), ".codex");
+  const source = join(ambientHome, "codex-security", "config.toml");
+  let configured: TomlTable = {};
+  try {
+    configured = parseToml(
+      await readFile(source, { encoding: "utf8", signal }),
+    );
+  } catch (error) {
+    if (!isRecord(error) || error["code"] !== "ENOENT") {
+      throw new CodexSecurityError(
+        `Cannot read Codex Security configuration at ${source}.`,
+        { cause: error },
+      );
+    }
+  }
+  const existing = configured["deep_scan"];
+  if (existing !== undefined && !isRecord(existing)) {
+    throw new CodexSecurityError(
+      `Codex Security configuration [deep_scan] at ${source} must be a TOML table.`,
+    );
+  }
+  const overrides: TomlTable = {};
+  for (const [name, key] of DEEP_SCAN_SETTINGS) {
+    const value = options[name];
+    if (value !== undefined) overrides[key] = value;
+  }
+  if (existing === undefined && Object.keys(overrides).length === 0) return;
+  const destination = join(codexHome, "codex-security", "config.toml");
+  if (destination === source && Object.keys(overrides).length === 0) return;
+  await mkdir(dirname(destination), { recursive: true, mode: 0o700 });
+  await writeFile(
+    destination,
+    stringifyToml({
+      ...configured,
+      deep_scan: { ...existing, ...overrides },
+    }),
+    { mode: 0o600, signal },
+  );
+}
+
 export async function initialCredentialsAvailable(
   environment: ProcessEnvironment,
   ambientHome: string,
@@ -1552,6 +1654,11 @@ async function scanPrompt(
   return [
     `Use the installed $codex-security:${skillName} skill at "$CODEX_SECURITY_PLUGIN_ROOT/skills/${skillName}/SKILL.md".`,
     "Run this Codex Security scan non-interactively.",
+    ...(mode === "deep"
+      ? [
+          'The SDK has already registered this scan. Call start_codex_security_deep_scan with { scanId: "$CODEX_SECURITY_SCAN_ID" }; never pass targetPath or create another scan.',
+        ]
+      : []),
     ...(skillName === "deep-security-scan"
       ? []
       : [
@@ -1618,6 +1725,7 @@ function scanRecipe(
   failOnSeverity?: SeverityLevel,
   knowledgeBasePaths?: string[],
   maxCostUsd?: number,
+  deepScan?: DeepScanOptions,
 ): JsonObject {
   return {
     repository,
@@ -1636,6 +1744,9 @@ function scanRecipe(
     ...(failOnSeverity === undefined ? {} : { failOnSeverity }),
     ...(knowledgeBasePaths === undefined ? {} : { knowledgeBasePaths }),
     ...(maxCostUsd === undefined ? {} : { maxCostUsd }),
+    ...(deepScan === undefined || Object.keys(deepScan).length === 0
+      ? {}
+      : { deepScan: { ...deepScan } }),
   };
 }