I am new to the kohana php framework. In the modules folder in kohana 3.1, there are many empty files extending the existing classes. Should I write my code in those empty files? 
If yes, do I have to make any changes in bootstrap? 
If not, where should I place these files? Should they be in a subfolder inside the Application directory or inside the modules directory?
Which all files will I have to copy from the modules to application?