diff --git a/Core/Manifest/ConfigManifest.php b/Core/Manifest/ConfigManifest.php
index be612e181..1f97ace0f 100644
--- a/Core/Manifest/ConfigManifest.php
+++ b/Core/Manifest/ConfigManifest.php
@@ -226,6 +226,7 @@ class ConfigManifest {
 
 		$finder = new ManifestFileFinder();
 		$finder->setOptions(array(
+			'min_depth' => 0,
 			'name_regex'    => '/(^|[\/\\\\])_config.php$/',
 			'ignore_tests'  => !$includeTests,
 			'file_callback' => array($this, 'addSourceConfigFile')
diff --git a/Core/Manifest/ManifestFileFinder.php b/Core/Manifest/ManifestFileFinder.php
index f081a6240..f5f3b4c71 100644
--- a/Core/Manifest/ManifestFileFinder.php
+++ b/Core/Manifest/ManifestFileFinder.php
@@ -39,6 +39,11 @@ class ManifestFileFinder extends FileFinder {
 			return false;
 		}
 
+		// Skip over the vendor directories
+		if (($depth == 1 || $depth == 2) && $basename == 'vendor') {
+			return false;
+		}
+
 		// If we're not in testing mode, then skip over any tests directories.
 		if ($this->getOption('ignore_tests') && $basename == self::TESTS_DIR) {
 			return false;
@@ -57,6 +62,8 @@ class ManifestFileFinder extends FileFinder {
 			&& !($this->getOption('include_themes') && $basename == THEMES_DIR)
 			&& !file_exists($pathname . '/' . self::CONFIG_FILE)
 			&& !file_exists($pathname . '/' . self::CONFIG_DIR)
+			&& $basename !== self::CONFIG_DIR // include a root config dir
+			&& !file_exists("$pathname/../" . self::CONFIG_DIR) // include all paths if a root config dir exists
 		);
 
 		if ($lackingConfig) {
diff --git a/View/ThemeManifest.php b/View/ThemeManifest.php
index ea2e9f36f..4f73011ed 100644
--- a/View/ThemeManifest.php
+++ b/View/ThemeManifest.php
@@ -154,7 +154,7 @@ class ThemeManifest implements ThemeList {
 		$path = '/'.implode('/', $themeParts);
 
 		// If this is in the project, add to beginning of list. Else add to end.
-		if ($themeParts[0] == $this->project) {
+		if ($themeParts && $themeParts[0] == $this->project) {
 			array_unshift($this->themes, $path);
 		}
 		else {