diff --git a/apps/desktop-shell/scripts/check-config.mjs b/apps/desktop-shell/scripts/check-config.mjs
index dbaba5999..1dc6062e0 100644
--- a/apps/desktop-shell/scripts/check-config.mjs
+++ b/apps/desktop-shell/scripts/check-config.mjs
@@ -220,6 +220,10 @@ const productionFileExtensions = new Set(['.json', '.mjs', '.plist', '.rs', '.to
 const productionSourceExcludedDirectories = new Set([
   'target',
 ]);
+const productionSourceExcludedRelativePaths = new Set([
+  'src-tauri/gen',
+  'src-tauri/permissions/autogenerated',
+]);
 const devScaffoldTerms = [
   'mo' + 'ck',
   'fa' + 'ke',
@@ -590,6 +594,11 @@ function assertCargoLockDirectDependency(
 function collectProductionSourceFiles(entry) {
   const stats = fs.statSync(entry);
   if (stats.isDirectory()) {
+    const relativePath = pathRelativeToDesktopShell(entry);
+    if (productionSourceExcludedRelativePaths.has(relativePath)) {
+      return [];
+    }
+
     const directory = entry.href.endsWith('/') ? entry : new URL(`${entry.href}/`);
     return fs
       .readdirSync(entry, { withFileTypes: true })
@@ -616,6 +625,18 @@ function collectProductionSourceFiles(entry) {
   return [entry];
 }
 
+function pathRelativeToDesktopShell(entry) {
+  const desktopShellRoot = new URL('../', import.meta.url);
+  return pathRelative(desktopShellRoot.pathname, entry.pathname);
+}
+
+function pathRelative(fromPath, toPath) {
+  return toPath
+    .slice(fromPath.length)
+    .replace(/^\/+/, '')
+    .replace(/\/$/, '');
+}
+
 const productionSourceFiles = productionSourceRoots.flatMap((root) =>
   collectProductionSourceFiles(root),
 );