Like everything else, modifying code of open-source tools has its cons and pros. The biggest advantage is of course an ability to customize the tool exactly to your needs. The problem is that it makes patching and upgrading impossible. This is the reason plugins exist - they do not break ability to patch the host product. So, if customization cannot be avoided even at the cost of losing ability to patch/upgrade - that would definitely work. Otherwise, plugins is probably the best approach.