Implement brevity penalty smoothing for PRO

As in Nakov et al (Coling 2012)
Added missing function call to for sort order check
Merge branch 'master' of github.com:moses-smt/mosesdecoder
add word alignment for OOV too. Exist for pb but not hiero model
Merge branch 'master' of github.com:moses-smt/mosesdecoder
Work to allow output search graph in HTK standard lattice format
More work on outputting HTK SLF.

Now, each arc emits exactly one word.
More work on outputting HTK lattice format
Add flag to output search graph in Kenneth's hypergraph format.
More work on outputting search graph as hypergraph
Deleted stale commented code
Output feature weights to a separate file when producing hypergraph
eclipse project files
WIP. Fix for incorrect alignment from moses_chart