fix(cli): support bulk-scan options and flexible CSV ordering

docker/entrypoint.sh

@@ -2,11 +2,61 @@
 
 set -eu
 
-if [ "${1:-}" = bulk-scan ]; then
-    case "${2:-}" in
-        --help|-h)
+bulk_scan_command=
+bulk_scan_input=
+bulk_scan_metadata=
+expects_option_value=
+
+for argument do
+    if [ "$argument" = -- ] && [ "$bulk_scan_command" = yes ]; then
+        printf '%s\n' 'codex-security: bulk-scan does not support the -- option terminator.' >&2
+        exit 2
+    fi
+
+    case "$argument" in
+        --help|-h|--llms|--llms-full|--schema|--version)
+            bulk_scan_metadata=yes
+            continue
+            ;;
+    esac
+
+    if [ "$expects_option_value" = yes ]; then
+        expects_option_value=
+        continue
+    fi
+
+    case "$argument" in
+        --)
+            break
+            ;;
+        bulk-scan)
+            if [ "$bulk_scan_command" = yes ]; then
+                bulk_scan_input=$argument
+            else
+                bulk_scan_command=yes
+            fi
             ;;
-        ""|-*)
+        --output-dir|--workers|--mode|--model|--effort|--provider|\
+            --knowledge-base|--max-attempts|--plugin-path|--python|\
+            --codex|--filter-output|--format|\
+            --scan-prompt-file|--post-scan-prompt-file|\
+            --token-limit|--token-offset)
+            expects_option_value=yes
+            ;;
+        -*)
+            ;;
+        *)
+            if [ "$bulk_scan_command" != yes ]; then
+                break
+            fi
+            bulk_scan_input=$argument
+            ;;
+    esac
+done
+
+if [ "$bulk_scan_command" = yes ] && [ "$bulk_scan_metadata" != yes ]; then
+    case "$bulk_scan_input" in
+        "")
             printf '%s\n' 'codex-security: bulk-scan requires a repository CSV; interactive discovery is not supported in this image.' >&2
             exit 2
             ;;

sdk/typescript/README.md

@@ -212,6 +212,7 @@ npx @openai/codex-security scan /path/to/repository --mode deep --workers 2 --su
 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
+npx @openai/codex-security bulk-scan --workers 4 --mode deep --max-attempts 3
 npx @openai/codex-security bulk-scan repositories.csv --output-dir /path/outside/repositories/security-scans --workers 4 --knowledge-base /path/to/threat-models --knowledge-base /path/to/architecture.pdf
 npx @openai/codex-security bulk-scan repositories.csv --output-dir /path/outside/repositories/security-scans --scan-prompt-file scan.md --post-scan-prompt-file follow-up.md
 npx @openai/codex-security scans list /path/to/repository
@@ -478,6 +479,11 @@ Private checkouts reuse your GitHub CLI sign-in without changing your global Git
 configuration. The selected repositories are saved to
 `<output-dir>/repositories.csv` for review or resumption.
 
+Interactive discovery accepts the same `--workers`, `--mode`, `--max-attempts`,
+`--model`, `--effort`, `--plugin-path`, `--python`, and `--codex` settings as
+CSV-driven scans. It prompts for the output directory; `--output-dir` is only
+valid when a repository CSV is supplied.
+
 To use an existing repository list or run in CI, pass a CSV with required `id`,
 `repository`, and `revision` columns. Revisions must be full commit hashes;
 optional `scope`, `mode`, and `prompt` columns customize individual scans:
@@ -633,6 +639,10 @@ device login remains in `state/`. For unattended scans, set `OPENAI_API_KEY`
 or `CODEX_API_KEY` instead. Set `GH_TOKEN` or `GITHUB_TOKEN` for private
 GitHub repositories.
 
+The container accepts the repository CSV before or after bulk-scan options.
+Interactive repository discovery remains disabled, including when global CLI
+options appear before `bulk-scan`.
+
 On Ubuntu hosts that restrict unprivileged user namespaces, an administrator
 can install the optional, narrowly scoped AppArmor profile once:
 

sdk/typescript/src/cli.ts

@@ -1424,36 +1424,9 @@ export async function main(
           let outputDir: string;
           let githubHost: string | undefined;
           if (args.input === undefined) {
-            let optionIndex = 1;
-            while (optionIndex < argv.length) {
-              const argument = argv[optionIndex]!;
-              if (
-                argument === "--model" ||
-                argument === "--effort" ||
-                argument === "--provider" ||
-                argument === "--codex" ||
-                argument === "--knowledge-base" ||
-                argument === "--scan-prompt-file" ||
-                argument === "--post-scan-prompt-file"
-              ) {
-                optionIndex += 2;
-              } else if (
-                argument.startsWith("--model=") ||
-                argument.startsWith("--effort=") ||
-                argument.startsWith("--provider=") ||
-                argument.startsWith("--codex=") ||
-                argument.startsWith("--knowledge-base=") ||
-                argument.startsWith("--scan-prompt-file=") ||
-                argument.startsWith("--post-scan-prompt-file=")
-              ) {
-                optionIndex += 1;
-              } else {
-                break;
-              }
-            }
-            if (argv[0] !== "bulk-scan" || optionIndex !== argv.length) {
+            if (options.outputDir !== undefined) {
               throw new Error(
-                "Run 'codex-security bulk-scan [--provider PROVIDER] [--model MODEL] [--effort EFFORT] [--codex KEY=VALUE] [--knowledge-base PATH]' to discover repositories, or provide a CSV and --output-dir.",
+                "--output-dir can only be used with a repository CSV; omit it to choose an output directory interactively.",
               );
             }
             const wizard = await runBulkScanWizard(

sdk/typescript/tests-ts/cli.test.ts

@@ -888,6 +888,10 @@ describe("CLI", () => {
       ["bulk-scan", "--codex", 'model_reasoning_effort="high"'],
       ["bulk-scan", '--codex=model_reasoning_effort="high"'],
       ["bulk-scan", "--model", "gpt-5.6-terra", "--effort", "high"],
+      ["bulk-scan", "--workers", "8", "--mode", "deep"],
+      ["bulk-scan", "--max-attempts=3", "--plugin-path", "./plugin"],
+      ["bulk-scan", "--python=python3"],
+      ["--format", "toon", "bulk-scan", "--workers", "8"],
       ["bulk-scan", "--knowledge-base", "/shared/threat-models"],
       [
         "bulk-scan",
@@ -944,6 +948,21 @@ describe("CLI", () => {
     expect(stdout.text()).toBe("");
   });
 
+  test("rejects an output directory without a repository CSV", async () => {
+    const stderr = capture();
+    expect(
+      await main(
+        ["bulk-scan", "--output-dir", "results"],
+        capture().stream,
+        stderr.stream,
+        dependencies(),
+      ),
+    ).toBe(2);
+    expect(stderr.text()).toContain(
+      "--output-dir can only be used with a repository CSV",
+    );
+  });
+
   test("exposes only typed, read-only SDK metadata over MCP", () => {
     const child = spawnSync(
       process.execPath,
@@ -2297,6 +2316,10 @@ describe("CLI", () => {
         ["bulk-scan", "--knowledge-base="],
         "--knowledge-base must not be empty",
       ],
+      [
+        ["bulk-scan", "--output-dir", "results", "--", "repositories.csv"],
+        "Unknown flag: --",
+      ],
       [["scan", ".", "--model="], "--model must not be empty"],
       [
         ["scan", ".", "--provider", "openrouter"],

sdk/typescript/tests-ts/container-entrypoint.test.ts

@@ -166,6 +166,34 @@ describe("customer container entrypoint", () => {
     },
   );
 
+  testPosix("accepts CSVs after global and bulk-scan options", async () => {
+    for (const arguments_ of [
+      ["bulk-scan", "--workers", "2", "/input/repositories.csv"],
+      ["bulk-scan", "bulk-scan", "--output-dir", "/output"],
+      [
+        "--format",
+        "toon",
+        "bulk-scan",
+        "--output-dir=/output",
+        "/input/repositories.csv",
+      ],
+    ] as const) {
+      const result = await runEntrypoint(arguments_);
+      expect(result.status).toBe(0);
+      expect(result.stderr).toBe("");
+      expect(result.stdout).toBe(
+        [
+          ...arguments_,
+          ...(appArmorRestrictsUserNamespaces &&
+          !usesCodexSecurityAppArmorProfile
+            ? ["--codex", "features.use_legacy_landlock=true"]
+            : []),
+          "",
+        ].join("\n"),
+      );
+    }
+  });
+
   testPosix(
     "preserves bulk-scan help without injecting scan configuration",
     async () => {
@@ -229,15 +257,35 @@ describe("customer container entrypoint", () => {
   testPosix(
     "rejects interactive discovery before starting the CLI",
     async () => {
-      const result = await runEntrypoint(["bulk-scan"]);
+      for (const arguments_ of [
+        ["bulk-scan"],
+        ["bulk-scan", "--workers", "8"],
+        ["bulk-scan", "--scan-prompt-file", "prompt.md"],
+        ["bulk-scan", "--post-scan-prompt-file", "post-prompt.md"],
+        ["--format", "json", "bulk-scan", "--mode", "deep"],
+      ] as const) {
+        const result = await runEntrypoint(arguments_);
+        expect(result.status).toBe(2);
+        expect(result.stdout).toBe("");
+        expect(result.stderr).toContain(
+          "interactive discovery is not supported",
+        );
+      }
+    },
+  );
 
+  testPosix("rejects unsupported bulk-scan option terminators", async () => {
+    for (const arguments_ of [
+      ["bulk-scan", "--output-dir", "/output", "--", "--help"],
+      ["bulk-scan", "--output-dir", "--", "--help"],
+    ] as const) {
+      const result = await runEntrypoint(arguments_);
       expect(result.status).toBe(2);
-      expect(result.stdout).toBe("");
-      expect(result.stderr).toBe(
-        "codex-security: bulk-scan requires a repository CSV; interactive discovery is not supported in this image.\n",
+      expect(result.stderr).toContain(
+        "does not support the -- option terminator",
       );
-    },
-  );
+    }
+  });
 
   testPosix("does not change non-scan commands", async () => {
     const result = await runEntrypoint(["--version"]);