diff --git a/check-eof.php b/check-eof.php
index 466d118..54c3b4c 100755
--- a/check-eof.php
+++ b/check-eof.php
@@ -5,10 +5,10 @@
  *
  * @package SMF
  * @author Simple Machines https://www.simplemachines.org
- * @copyright 2022 Simple Machines and individual contributors
+ * @copyright 2025 Simple Machines and individual contributors
  * @license https://www.simplemachines.org/about/smf/license.php BSD
  *
- * @version 2.1.0
+ * @version 3.0 Alpha 4
  */
 
 // Stuff we will ignore.
@@ -18,9 +18,6 @@
 	'./tests/',
 	'./vendor/',
 	'./.git',
-	'./Sources/minify/',
-	'./Sources/ReCaptcha/',
-	'./ZxcvbnPhp/',
 
 	// We will ignore Settings.php if this is a live dev site.
 	'./Settings.php',
@@ -64,4 +61,4 @@
 } catch (Exception $e) {
 	fwrite(STDERR, $e->getMessage() . "\n");
 	exit(1);
-}
\ No newline at end of file
+}
diff --git a/check-smf-license.php b/check-smf-license.php
index d444e32..d0ce928 100755
--- a/check-smf-license.php
+++ b/check-smf-license.php
@@ -5,52 +5,28 @@
  *
  * @package SMF
  * @author Simple Machines https://www.simplemachines.org
- * @copyright 2024 Simple Machines and individual contributors
+ * @copyright 2025 Simple Machines and individual contributors
  * @license https://www.simplemachines.org/about/smf/license.php BSD
  *
- * @version 3.0 Alpha 1
+ * @version 3.0 Alpha 4
  */
 
 // Stuff we will ignore.
 $ignoreFiles = [
-	// Index files.
-	'\./attachments/index\.php',
-	'\./avatars/index\.php',
-	'\./avatars/[A-Za-z0-9]+/index\.php',
-	'\./cache/index\.php',
-	'\./custom_avatar/index\.php',
-	'\./Packages/index\.php',
-	'\./Packages/backups/index\.php',
-	'\./Smileys/[A-Za-z0-9]+/index\.php',
-	'\./Smileys/index\.php',
-	'\./Sources/index\.php',
-	'\./Sources/[\w/]+/index\.php',
-	'\./other/Schema/[\w/]+/*\.php',
-	'\./Themes/default/index\.php',
-	'\./Themes/default/[\w/]+/index\.php',
-	'\./Themes/index\.php',
+	// Index files in subdirectories.
+	'\./(?:\w+/)+\bindex\.php',
 
 	// Language Files are ignored as they don't use the License format.
-	'./Themes/default/languages/[A-Za-z0-9]+\.english\.php',
-	'./Languages/en_US/[A-Za-z0-9]+\.php',
-	'./Themes/default/languages/en_US/[A-Za-z0-9]+\.php',
-	'\./Languages/index\.php',
+	'./Themes/default/languages/',
+	'\./Languages/',
 
 	// Cache and miscellaneous.
 	'\./cache/',
-	'\./other/db_last_error\.php',
-	'\./other/update_[A-Za-z0-9_]+\.php',
 	'\./tests/',
 	'\./vendor/',
 
-	// Minify Stuff.
-	'\./Sources/minify/',
-
-	// random_compat().
-	'\./Sources/random_compat/',
-
-	// ReCaptcha Stuff.
-	'\./Sources/ReCaptcha/',
+	// Everything in other except install.php, upgrade.php, Settings.php and Settings_bak.php.
+	'\./other/(?!install|upgrade|Settings)\w+\.php',
 
 	// We will ignore Settings.php if this is a live dev site.
 	'\./Settings\.php',
diff --git a/runTools.sh b/runTools.sh
index 37ac350..51b4c47 100644
--- a/runTools.sh
+++ b/runTools.sh
@@ -1,9 +1,6 @@
 #!/bin/bash
 
 find . -type f -name "*.php" -print0 \
-    -o -path "./Sources/minify" -prune \
-    -o -path "./Sources/random_compat" -prune \
-    -o -path "./Sources/ReCaptcha" -prune \
   | xargs -0 -n1 -P4 php -l \
   | (! grep -v "No syntax errors detected" )
 
@@ -11,4 +8,4 @@ php check-signed-off.php
 php check-eof.php
 php check-smf-license.php
 php check-smf-languages.php
-php check-version.php
\ No newline at end of file
+php check-version.php
diff --git a/secure-vendor-dir.php b/secure-vendor-dir.php
new file mode 100644
index 0000000..d1e0692
--- /dev/null
+++ b/secure-vendor-dir.php
@@ -0,0 +1,34 @@
+<?php
+
+/**
+ * Simple Machines Forum (SMF)
+ *
+ * @package SMF
+ * @author Simple Machines https://www.simplemachines.org
+ * @copyright 2025 Simple Machines and individual contributors
+ * @license https://www.simplemachines.org/about/smf/license.php BSD
+ *
+ * @version 3.0 Alpha 4
+ */
+
+$dirs = ['./vendor'];
+
+$iterator = new RecursiveIteratorIterator(
+	new RecursiveDirectoryIterator(
+		'./vendor',
+		RecursiveDirectoryIterator::SKIP_DOTS | FilesystemIterator::UNIX_PATHS,
+	),
+	RecursiveIteratorIterator::SELF_FIRST
+);
+
+foreach ($iterator as $item) {
+	if ($item->isDir()) {
+		$dirs[] = $item->getPathname();
+	}
+}
+
+foreach ($dirs as $key => $dir) {
+	if (!file_exists($dir . '/index.php')) {
+		copy('./Sources/index.php', $dir . '/index.php');
+	}
+}