Another try at fixing the include/exclude logic

src/IterableCodeExtractor.php

@@ -161,8 +161,6 @@ protected static function containsMatchingChildren( SplFileInfo $dir, array $mat
 		$root_relative_path = str_replace( static::$dir, '', $dir->getPathname() );
 
 		foreach ( $matchers as $path_or_file ) {
-			$path_or_file = ltrim( $path_or_file, '/' );
-
 			// If the matcher contains no wildcards and the path matches the start of the matcher.
 			if (
 				'' !== $root_relative_path &&
@@ -206,21 +204,26 @@ public static function getFilesFromDirectory( $dir, array $include = [], array $
 				function ( $file, $key, $iterator ) use ( $include, $exclude, $extensions ) {
 					/** @var RecursiveCallbackFilterIterator $iterator */
 					/** @var SplFileInfo $file */
+
+					// Normalize include and exclude paths.
+					$include = array_map( 'static::trim_leading_slash', $include );
+					$exclude = array_map( 'static::trim_leading_slash', $exclude );
+
 					// If no $include is passed everything gets the weakest possible matching score.
 					$inclusion_score = empty( $include ) ? 0.1 : static::calculateMatchScore( $file, $include );
 					$exclusion_score = static::calculateMatchScore( $file, $exclude );
 
 					// Always include directories that aren't excluded.
-					if ( $file->isDir() && 0 === $exclusion_score ) {
+					if ( 0 === $exclusion_score && $iterator->hasChildren() ) {
 						return true;
 					}
 
-					if ( $file->isDir() && ( 0 === $inclusion_score || $exclusion_score > $inclusion_score ) ) {
+					if ( ( 0 === $inclusion_score || $exclusion_score > $inclusion_score ) && $iterator->hasChildren() ) {
 						// Always include directories that may have matching children even if they are excluded.
 						return static::containsMatchingChildren( $file, $include );
 					}
 
-					return ( $file->isFile() && in_array( $file->getExtension(), $extensions, true ) );
+					return ( ( $inclusion_score >= $exclusion_score ) && $file->isFile() && in_array( $file->getExtension(), $extensions, true ) );
 				}
 			),
 			RecursiveIteratorIterator::CHILD_FIRST
@@ -239,4 +242,14 @@ function ( $file, $key, $iterator ) use ( $include, $exclude, $extensions ) {
 
 		return $filtered_files;
 	}
+
+	/**
+	 * Trim leading slash from a path.
+	 *
+	 * @param string $path Path to trim.
+	 * @return string Trimmed path.
+	 */
+	private static function trim_leading_slash( $path ) {
+		return ltrim( $path, '/' );
+	}
 }