changed to collapsing tree instead of matrix, other refactoring as well
Changed to stem-hy and improved modularity
added chopTree
Merge pull request #2 from marchtemp/stemTree

added chopTree, encapsulated chopping tree into new class
preparing for new testing and changes to chop
chopTree check
fixed chopTree
Merge pull request #3 from marchtemp/stemTree

fixed chopTree to account for clearing tree file
getting ready for large reorganization
new chopTree
Tentatively completed stem.py, stemParse, and outputGen refactoring
preparing to pull new chopTree
Merge pull request #4 from marchtemp/stemTree

new chopTree
getting ready to merge tree, stem, and groups branches