Upgrade to commons-io 2.4

In order to maintain backwards compatibility we need to keep IOUtils the
same as in commons-io 1.4. This code is backwards compatible, however
most of the methods have been deprecated and should instead use the
org.apache.commons.io.IOUtils version instead.
Merge pull request #1135 from christ66/commons-io-up

Upgrade to commons-io 2.4