Moved rule-to-tree mapping features to Tree.java
Now prints complete target-side tree with mapping using %t
Moved TestSetFilter from thrax, added loose filtering (for use with segmentation lattices)

When decoding with run-time segmented lattices (for handling OOVs), you can't use fast or
exact filtering. Loose filtering works by allowing grammar rules to partially match words
(effectively loosening the stricter "exact" requirements).
Fixed selection of grammar file for tuning and testing
Toggle packing from the command line
Now sorts and uniqs LM file before building LM
Updated test cases, added loose filtering to pipeline
Updated filtering error message
Updated thrax with version with alignments
Added feature computing source and target side lengths and pair lengths
Merge branch 'master' of github.com:joshua-decoder/joshua into devel