Commenting to explain what I'm doing

wp-sw-cache/wp-sw-cache-main.php

@@ -32,25 +32,32 @@ class SW_Cache_Main {
   public function write_sw() {
 
     $files = get_option('wp_sw_cache_files');
-    $file_keys = array();
     if(!$files) {
       $files = array();
     }
+
+    // Will contain items like 'style.css' => {filemtime() of style.css}
+    $file_keys = array();
+
+    // Ensure that every file directed to be cached still exists
     foreach($files as $index=>$file) {
       $tfile = get_template_directory().'/'.$file;
 
       if(file_exists($tfile)) {
+        // Use file's last change time in name hash so the SW is updated if any file is updated
         $file_keys[get_template_directory_uri().'/'.$file] = filemtime($tfile);
       }
     }
 
-    $file_keys = array_keys($file_keys);
+    // Serialize the entire array so we match file with time
+    // This will catch file updates done outside of admin (like updating via FTP)
     $name = md5(serialize($file_keys));
     self::update_version($name);
 
+    // Template content into the JS file
     $contents = file_get_contents(dirname(__FILE__).'/lib/service-worker.js');
     $contents = str_replace('$name', $name, $contents);
-    $contents = str_replace('$files', json_encode($file_keys), $contents);
+    $contents = str_replace('$files', json_encode(array_keys($file_keys)), $contents);
     $contents = str_replace('$debug', get_option('wp_sw_cache_debug') ? 'true' : 'false', $contents);
     echo $contents;
   }