shuffling of hypergraphs
changes to protecting specified patterns (with example patterns)
Implement shuffling correctly
Merge branch 'master' of github.com:moses-smt/mosesdecoder
Incremental scoring of hypotheses.

Don't score full score vectors in hypotheses, just
the increments. The full score breakdowns (required for
nbest lists) are calculated lazily.
Merge branch 'master' of https://github.com/moses-smt/mosesdecoder
Merge ../mosesdecoder into hieu
move notice about czech prefixes to share/README
Merge ../mosesdecoder into hieu