Fixes to hypergraph and htk outputs, better cmd line help.

Mixing boost paths and strings is bad.
Leaks in htk output.
assert that should be an exception
Merge branch 'master' of github.com:moses-smt/mosesdecoder
Merge branch 'master' of github.com:moses-smt/mosesdecoder
Merge branch 'master' of github.com:moses-smt/mosesdecoder
word alignment from server, thanks to Jyotesh Choudhari