FileHandler Changed to Using Accessors

Created by: osbornjd

In conjunction with the recommendation from PR 408, this PR changes the design of the FileHandler slightly to use default constructors and then set the source and destination files via accessors, rather than setting them in the constructor.

This commit also addresses the bug pointed out by @jayjaybillings in issue 409.

There is also a commit that adds two example files that demonstrate how the commands API works for the user.