> How do you detect the modifications? We compute the hashes of the files regularly. If only one character in a file changes, his hash will change.

Does this include HTTP headers? For instance a yay.js framework that helps people print 'yay' to the console could return:

  HTTP/1.1 301 MOVED PERMANENTLY
  LOCATION: http://evil.evil/evil.js
  
  console.log('yay!');