Merging code from Dev wordsi into master

[fozziethebeat]

Dev-Wordsi contains a multitude of small fixes and a bulk of new code centered around consensus clustering. This also makes a significant change to the Assignments interface to make it easier and less cumbersome to use.

The new Consensus Clustering code relies on a new object called a partition, which is an easy to use representation of a clustering solution that includes some addiition helper methods not useful to general clustering Assignments. The Consensus merging algorithms use a comparison function between partitions and a combining algorithm to generate an improved Partition.

In addition to this major update, there are smaller bug fixes and minor refactorings needed within the consensus clustering code.

[davidjurgens]

Overall, the changes look good. I have a few concerns where the graph package and some of the matrix-as-graph classes overlap in functionality. It would be good to present a common theme for those.

[fozziethebeat]

I still need to go through and fix the javadocs and the minor suggestions, but I put in my thoughts on some of the larger suggestions.

[fozziethebeat]

Most of the javadoc and simple cleaning changes fixed. There's still a few more to be handled.