Removes Apache IO and cleans more code

The dependency of Apache Commons IO has been removed and replaced with a FileUtils class. The new FileUtils class mimics the properties of the old one, however, it uses [java.nio.file.Files](http://docs.oracle.com/javase/7/docs/api/java/nio/file/Files.html).

Also the following changes have been made:
* Infer generic types (Class<?>) in most classes in the utils package
* Organised imports in most classes in the utils package, and in the YAMLDataSource class
* Made sure input streams are closed after use in the ResourceUtils class