Core file adjustments

In my path towards learning opencart fully I have run a road block in regards to the core files. I have seen many extensions that state it may not work with modded core files. Well I have wondered what is considered an opencart core file? I have seen and purchased a few themes but I still would like to use some awesome extensions but I am afraid to to go that route till I fully understand what I am doing

Core files, in my opinion are controllers, models, languages, and libraries. Typically you won't need to change these at all unless your well versed in MVC and PHP. If your simply looking to use different themes this shouldn't really be too much of an issue, however you may run into the odd hick-up here and there ~~ from my experience extension authors will gladly provide a certain level of support for free, after that it would become an assisted install which you would pay a small amount extra for.