Christopher Sheaf - Version 0.7

First real source code commit.
Things that are working:
- Dependency resolution (Tasks are run only once their dependencies are satisfied)
- Parsing tasks and parameters from XML.
- The SequenceVariationTask, which generates an .fst full of variations given an .fst containing an initial sequence.
Christopher Sheaf - Version 0.71

Added the modified .R code, which now reads all arguments from the command line, and names sequences with the changes made from the original.