fix: normalize Windows configuration paths

sdk/typescript/_bundled_plugin/references/config-preflight.md

@@ -16,7 +16,7 @@ For standard and diff scans, a passed `delegated_workers` check means the runtim
 
 When `CODEX_SECURITY_CONFIG_PATH` is set, add `--config "$CODEX_SECURITY_CONFIG_PATH"` in POSIX shells or `--config "$env:CODEX_SECURITY_CONFIG_PATH"` in PowerShell. The CLI provides this sanitized, shell-readable copy of the active worker configuration because the credential-bearing `CODEX_HOME` is intentionally inaccessible to repository-influenced commands. Do not substitute an ambient Codex home in that case.
 
-Otherwise, the helper discovers Codex config paths itself from `--cwd`, which defaults to the current working directory. It reads `/etc/codex/config.toml`, then `$CODEX_HOME/config.toml`, resolves `project_root_markers`, checks the matching `[projects."<absolute-project-root>"].trust_level`, and loads trusted project `.codex/config.toml` layers from the project root down to `--cwd`. It does not load project layers unless the user config marks that project root as `trusted`.
+Otherwise, the helper discovers Codex config paths itself from `--cwd`, which defaults to the current working directory. It reads `/etc/codex/config.toml` on Unix-like hosts or `%ProgramData%\OpenAI\Codex\config.toml` on Windows, then `$CODEX_HOME/config.toml`, resolves `project_root_markers`, checks the matching `[projects."<absolute-project-root>"].trust_level`, and loads trusted project `.codex/config.toml` layers from the project root down to `--cwd`. It does not load project layers unless the user config marks that project root as `trusted`.
 
 When the current Codex CLI session selected `-p/--profile <name>`, pass `--codex-config-profile <name>`. Current Codex loads `$CODEX_HOME/<name>.config.toml` above the base user config and below trusted project config, so the helper uses that layer for project-root markers, trust, and capability values before it discovers project config. A missing profile file is an empty layer, matching the CLI. Embedded `[profiles.<name>]` lookup remains only for older Codex configs that select `profile` without the CLI flag. Project-local `profile` and `profiles` values are ignored. For session-only CLI overrides or other effective config values that cannot be recovered from config paths, pass `--effective-config <path>=<json-value>`.
 

sdk/typescript/_bundled_plugin/scripts/config_preflight.py

@@ -20,7 +20,16 @@
 PLUGIN_ROOT = Path(__file__).resolve().parents[1]
 DEFAULT_REGISTRY = PLUGIN_ROOT / "preflight" / "capability-profiles.toml"
 DEFAULT_CODEX_HOME = Path(os.environ.get("CODEX_HOME", "~/.codex")).expanduser()
-SYSTEM_CONFIG = Path("/etc/codex/config.toml")
+
+
+def default_system_config() -> Path:
+    if os.name == "nt":
+        program_data = os.environ.get("ProgramData", r"C:\ProgramData")
+        return Path(program_data) / "OpenAI" / "Codex" / "config.toml"
+    return Path("/etc/codex/config.toml")
+
+
+SYSTEM_CONFIG = default_system_config()
 DEFAULT_CONFIG = DEFAULT_CODEX_HOME / "config.toml"
 VALID_SEVERITIES = {"block", "warn", "suggest"}
 VALID_MULTI_AGENT_OWNERS = {"native", "codex-bridge"}
@@ -244,6 +253,16 @@ def project_trust_level(
         if not isinstance(projects, dict):
             continue
         project = projects.get(str(project_root))
+        if not isinstance(project, dict) and os.name == "nt":
+            project_key = os.path.normcase(os.path.realpath(project_root))
+            project = next(
+                (
+                    value
+                    for path, value in projects.items()
+                    if os.path.normcase(os.path.realpath(path)) == project_key
+                ),
+                None,
+            )
         if not isinstance(project, dict):
             continue
         trust_level = project.get("trust_level")

sdk/typescript/src/api.ts

@@ -100,6 +100,7 @@ import {
   codexSecurityHasStoredFileCredentials,
   codexSecurityStateDirectory,
   createIsolatedHome,
+  expandHome,
   importAmbientAuth,
   prepareCodexSecurityCredentialHome,
   preserveCodexSecurityPluginRegistration,
@@ -2101,8 +2102,10 @@ async function prepareDeepScanConfig(
   options: DeepScanOptions,
   signal: AbortSignal,
 ): Promise<void> {
-  const ambientHome =
-    environmentValue(environment, "CODEX_HOME") ?? join(homedir(), ".codex");
+  const ambientHome = expandHome(
+    environmentValue(environment, "CODEX_HOME") ?? join(homedir(), ".codex"),
+    environment,
+  );
   const source = join(ambientHome, "codex-security", "config.toml");
   let configured: TomlTable = {};
   try {
@@ -2128,14 +2131,15 @@ async function prepareDeepScanConfig(
     const value = options[name];
     if (value !== undefined) overrides[key] = value;
   }
+  const sharedConfig = await sameExistingPath(source, destination);
   const hasOverrides = Object.keys(overrides).length > 0;
   if (existing === undefined && !hasOverrides) {
-    if (destination !== source) {
+    if (!sharedConfig) {
       await rm(destination, { force: true });
     }
     return;
   }
-  if (destination === source && !hasOverrides) return;
+  if (sharedConfig && !hasOverrides) return;
   await mkdir(dirname(destination), { recursive: true, mode: 0o700 });
   await writeFile(
     destination,
@@ -2147,6 +2151,15 @@ async function prepareDeepScanConfig(
   );
 }
 
+async function sameExistingPath(left: string, right: string): Promise<boolean> {
+  if (left === right) return true;
+  const [canonicalLeft, canonicalRight] = await Promise.all([
+    realpath(left).catch(() => null),
+    realpath(right).catch(() => null),
+  ]);
+  return canonicalLeft !== null && canonicalLeft === canonicalRight;
+}
+
 export function createSecurity(
   config: CodexSecurityConfig = {},
 ): CodexSecurity {

sdk/typescript/src/bulk-scan-discovery.ts

@@ -8,6 +8,7 @@ import { promisify } from "node:util";
 import { confirm, input, search } from "@inquirer/prompts";
 import { Octokit } from "@octokit/core";
 import Papa from "papaparse";
+import { expandHome } from "./runtime.js";
 import { resolveTrustedExecutable } from "./trusted-executable.js";
 
 const execFile = promisify(execFileCallback);
@@ -171,9 +172,11 @@ export async function runBulkScanWizard(
 
   const outputDir = resolve(
     dependencies.currentDirectory(),
-    await prompt.input(
-      "Where should scan results be saved?",
-      "./security-scans",
+    expandHome(
+      await prompt.input(
+        "Where should scan results be saved?",
+        "./security-scans",
+      ),
     ),
   );
   const inputPath = join(outputDir, "repositories.csv");

sdk/typescript/src/cli.ts

@@ -586,11 +586,14 @@ async function readPromptFiles(
   const [scanPrompt, postScanPrompt] = await Promise.all([
     scanPromptFile === undefined
       ? undefined
-      : readRegularInputFile(resolve(directory, scanPromptFile), repository),
+      : readRegularInputFile(
+          resolveCliPath(directory, scanPromptFile),
+          repository,
+        ),
     postScanPromptFile === undefined
       ? undefined
       : readRegularInputFile(
-          resolve(directory, postScanPromptFile),
+          resolveCliPath(directory, postScanPromptFile),
           repository,
         ),
   ]);
@@ -646,6 +649,10 @@ async function readRegularInputFile(
   }
 }
 
+export function resolveCliPath(directory: string, value: string): string {
+  return resolve(directory, expandHome(value));
+}
+
 interface ScanArguments extends DeepScanOptions {
   auth?: ScanAuthMode;
   verbose?: boolean;
@@ -901,7 +908,9 @@ export async function runCodexSkillCommand(
     if (name.toUpperCase() === "CODEX_HOME") delete environment[name];
   }
   if (configuredHome?.trim()) {
-    environment["CODEX_HOME"] = resolve(expandHome(configuredHome));
+    environment["CODEX_HOME"] = resolve(
+      expandHome(configuredHome, processEnvironment),
+    );
   }
   const invocation = spawn(command.command, [...args], {
     env: environment,
@@ -1281,7 +1290,7 @@ export async function main(
     }),
     output: z.record(z.string(), z.unknown()).optional(),
     async run({ args, format }) {
-      const repository = resolve(
+      const repository = resolveCliPath(
         dependencies.currentDirectory(),
         args.repository ?? ".",
       );
@@ -1330,26 +1339,25 @@ export async function main(
       output: z.record(z.string(), z.unknown()).optional(),
       async run({ args, format, options }) {
         const directory = dependencies.currentDirectory();
+        const scanRoot =
+          options.scanRoot === undefined
+            ? undefined
+            : resolveCliPath(directory, options.scanRoot);
         const repository =
-          options.scanRoot !== undefined && args.repository === undefined
+          scanRoot !== undefined && args.repository === undefined
             ? undefined
-            : resolve(directory, args.repository ?? directory);
+            : resolveCliPath(directory, args.repository ?? directory);
         return presentHistory(
           await history([
             "list-scans",
             ...(repository === undefined ? [] : ["--repository", repository]),
-            ...(options.scanRoot === undefined
-              ? []
-              : ["--scan-root", resolve(directory, options.scanRoot)]),
+            ...(scanRoot === undefined ? [] : ["--scan-root", scanRoot]),
           ]),
           "list",
           format,
           {
             repository,
-            scanRoot:
-              options.scanRoot === undefined
-                ? undefined
-                : resolve(directory, options.scanRoot),
+            scanRoot,
           },
         );
       },
@@ -2168,7 +2176,10 @@ export async function main(
             "git",
             [
               "-C",
-              resolve(dependencies.currentDirectory(), args.repository ?? "."),
+              resolveCliPath(
+                dependencies.currentDirectory(),
+                args.repository ?? ".",
+              ),
               "rev-parse",
               "--path-format=absolute",
               "--git-path",
@@ -2346,8 +2357,8 @@ export async function main(
                 "--output-dir is required with a repository CSV.",
               );
             }
-            inputPath = resolve(currentDirectory, args.input);
-            outputDir = resolve(currentDirectory, options.outputDir);
+            inputPath = resolveCliPath(currentDirectory, args.input);
+            outputDir = resolveCliPath(currentDirectory, options.outputDir);
           }
           const result = await runMultiscan({
             inputPath,
@@ -2443,20 +2454,20 @@ export async function main(
         if (scanDir === undefined) return;
         exitCode = await runExport(
           {
-            scanDir: resolve(currentDirectory, scanDir),
+            scanDir: resolveCliPath(currentDirectory, scanDir),
             format: options.exportFormat,
             output:
               options.output === "-"
                 ? "-"
-                : resolve(
+                : resolveCliPath(
                     currentDirectory,
                     options.output ??
                       EXPORT_DEFAULT_OUTPUTS[options.exportFormat],
                   ),
             sourceRoot:
               options.sourceRoot === undefined
                 ? undefined
-                : resolve(currentDirectory, options.sourceRoot),
+                : resolveCliPath(currentDirectory, options.sourceRoot),
             pythonPath: options.python,
           },
           output,
@@ -3272,7 +3283,7 @@ async function runSkill(
         !staysWithinWindowsDeviceRoot(input, rawDeviceRoot) ||
         localDeviceRoot !== normalizedDeviceRoot);
     if (!windowsNetworkPath) {
-      const path = resolve(directory, input);
+      const path = resolveCliPath(directory, input);
       const metadata = await lstat(path, { bigint: true }).catch(
         (error: unknown) => {
           if (

sdk/typescript/src/runtime.ts

@@ -124,10 +124,17 @@ export function codexSecurityStateDirectory(
   environment: ProcessEnvironment = process.env,
 ): string {
   const configured = environmentValue(environment, "CODEX_SECURITY_STATE_DIR");
-  if (configured !== undefined) return resolve(expandHome(configured));
+  if (configured !== undefined) {
+    return resolve(expandHome(configured, environment));
+  }
   const codexHome =
     environmentValue(environment, "CODEX_HOME") ?? join(homedir(), ".codex");
-  return resolve(expandHome(codexHome), "state", "plugins", "codex-security");
+  return resolve(
+    expandHome(codexHome, environment),
+    "state",
+    "plugins",
+    "codex-security",
+  );
 }
 
 export function codexSecurityCredentialHome(
@@ -2023,11 +2030,13 @@ export function resolveCodexCommand(
   environment: ProcessEnvironment = process.env,
 ): CodexCommand {
   const configured = environmentValue(environment, "CODEX_CLI_PATH");
+  const expanded =
+    configured === undefined ? undefined : expandHome(configured, environment);
   if (
-    configured &&
-    (process.platform !== "win32" || /\.(?:exe|com)$/iu.test(configured))
+    expanded &&
+    (process.platform !== "win32" || /\.(?:exe|com)$/iu.test(expanded))
   ) {
-    return { command: resolve(configured) };
+    return { command: resolve(expanded) };
   }
 
   const platform = process.platform === "android" ? "linux" : process.platform;
@@ -2482,7 +2491,9 @@ async function usablePython(
   signal?: AbortSignal,
 ): Promise<string | null> {
   const command = await resolveTrustedExecutable(
-    isPythonPathCandidate(candidate) ? expandHome(candidate) : candidate,
+    isPythonPathCandidate(candidate)
+      ? expandHome(candidate, environment)
+      : candidate,
     environment,
     protectedRoot,
   );
@@ -2548,10 +2559,20 @@ async function sameFile(left: string, right: string): Promise<boolean> {
   }
 }
 
-export function expandHome(value: string): string {
-  if (value === "~") return homedir();
-  if (value.startsWith("~/") || value.startsWith("~\\")) {
-    return join(homedir(), value.slice(2));
+export function expandHome(
+  value: string,
+  environment: ProcessEnvironment = process.env,
+): string {
+  const home =
+    (process.platform === "win32"
+      ? environmentValue(environment, "USERPROFILE") ??
+        environmentValue(environment, "HOME")
+      : environmentValue(environment, "HOME") ??
+        environmentValue(environment, "USERPROFILE")) ?? homedir();
+  if (value === "~") return home;
+  if (value.startsWith("~/")) return join(home, value.slice(2));
+  if (value.startsWith("~\\")) {
+    return join(home, ...value.slice(2).split("\\"));
   }
   return value;
 }