I don't have included KCFinder in every GIT repository, I like add it like other dependencies (using Composer for PHP or Bower for JS/CSS).

Because KCFinder is combination of both and is used over HTTP, I've added it via Bower.
However I need custom PHP config and I have two ways:

• fork a repository of KCFinder for each config
• enable config PHP file outside the KCFinder repo

I like the second option, so I've made a conditional require inside conf/config.php.
Now when I install KCFinder via bower, I can create custom script kcfinder-config.php in the root of bower libraries and everything works fine, is customized and I don't need new repositories of KCFinder for each project where I use it :)