Finished unit testing and confirming functionality

Much of the old code is ready to be removed.
Merge branch 'v3-template' of github.com:veg/hyphy into v3-template

Updating branch before finishing refactoring and pushing changes.
Finished cleaning, confirmed coverage
Moved the methods peeled from the site class

Put them in site_helpers
Updated cpp file intro text
Attaching unit test file
Cleaning unit test file
Merge pull request #198 from mdsmith/v3-template

Site class refactoring