added square format for phylipfile. made command work with list files containing unique and redundant sequences
a lot of new input parameters in rf module, implemented a pruning system in the rf tree plus some runtime performance improvements
paralellized parsimony, unifrac.unweighted, phylo.diversity, indicator commands for windows.
added sparcc command.  fixed bug in remove.groups that removed all groups if you had a typo in the group name. fixed order parameter in sff.multiple.
cluster.split was not sorting the list file in order of abundance
added count file to create.database command. corrected for change to get.oturep changing order of members in otu to reflect the names file format.  That change caused the create.database command to fail to find otus
added make.lookup command.
cleaned up what is printed to screen
updated default parameters. These are giving better error rates.
added modify names parameter to set.dir
changed how rarefaction commands find the lci and hci. they now save values from each iter at each frequency, report values at the .025 and .975.
changes while testing
Merge branch 'upstream-master'
Merge branch 'upstream-dev-ml'

Conflicts:
	classifysharedcommand.cpp
	randomforest.cpp