[eluser]ketema[/eluser]
I have a similar problem. First to answer your question: You can't just click run on a controller or view file and expect to debug it. CI applications start at the index.php in your root application directory and have to include all the CI framework stuff. You can use xdebug if your IDE supports it. I have xdebug set up correctly, but you will run into the same problem I have once you get it set up.
UPDATE EDIT
I had a symlink issue. Disregard below. Once you set up xdebug properly breakpoints will work.
Controllers and Views are just classes that extend CI classes...so when I set break points inside my class functions the debugger never stops on them. It took me a while to understand why. I need to be able to stop when the INSTANCE of my class is executing my function. It will never stop on the class definition code. But Where the heck would that be in the CI framework?
To summarize:
How can you get a debugger to stop on a breakpoint in a controller file when an instance of that controller is created and calls a function that you want to stop within ?