A PHP function to recursively get the files and hashes of all files in a given directory and in its subdirectories.

get_all_file_hashes.php

<?php

function get_all_file_hashes( $directory, $relative_to = null ) {
	$directory           = rtrim( $directory, '/\\' ) . '/';
	$relative_to         = $relative_to ? $relative_to : $directory;
	$preg_quote_relative = preg_quote( $relative_to, '#' );
	$files               = glob( $directory . '*' );
	$return              = array();

	foreach ( $files as $file ) {
		if ( is_dir( $file ) ) {
			$return = array_merge( $return, get_all_file_hashes( $file, $relative_to ) );
		} else {
			$local_path = preg_replace( '#^' . $preg_quote_relative . '#', '', $file );
			$return[ $local_path ] = md5_file( $file );
		}
	}
	
	return $return;
}

Usage example:

print_r( get_all_file_hashes( getcwd() ) );