Remove --OutputNTLengths from extract-rules, etc.

The option isn't used in master and the output is compatible with the
current rule table format.  If anyone wants this in master it should
probably be fixed in the span-length branch then merged.
Added known issues to the m4m README.
Merge branch 'master' of github.com:moses-smt/mosesdecoder
Re-enable unit tests. They all pass.
Merge branch 'master' into sparse-reordering
Renamed