small simplification of recursive CYK+

(following Chris Dyer's suggestion and Phil's refactoring in S2T decoder)
move n-best code for phrase-based from IOWrapper to Manager
move OutputLatticeSamples() for phrase-based from IOWrapper to Manager
delete OutputNBest() in IOWrapper
Add score-stsg, a program for scoring STSG extract files
move n-best code for phrase-based from IOWrapper to ChartManager
change for thot integration
add OutputNBest() as abstract method to BaseManager. Tighten up framework
Merge branch 'merge-cmd'
comment out running script. Need to get git version to insert into exec