bugfix: sentence length limit wasn't working for lattices, now hard-coded to 200 nodes

this should be a command-line option though
MERT now skips nonconforming lines in the nbest output file.

Added this as a quickfix to an nbest file which contained the lines

"Java HotSpot(TM) 64-Bit Server VM warning: Attempt to allocate stack guard pages failed."

causing a huge, expensive mert run to fail.
bugfix: mbr bleu had duplicate cachecmd name
moved bleu summary computation into a function
now permits a --joshua-args flag for passing arbitrary arguments to the decoder invocations
now computes bleu summary (at test/final-bleu*) after each optimization run, instead of just at the end
automatically figures out nbest or plain format (sigh)
bugfix: need to prepend a space to JOSHUA_ARGS for backwards-compatibility with old cachecmd runs
added missing %e reduction for empty sentences
When decoding with lattices, we now output the source sentence (= the path we took
through the lattice) with the n-best list.
bugfix: pipeline was fixing test run grammars to width 12, instead of 20
for lattices, we now extract the source path, place it in the test run directory, and use it when producing the analysis (instead of the basically useless lattice source)
added pipeline summary script
altered default thrax features
updated pipeline to tune outside grammars present in joshua.config file template
bugfix in parsing: makes directory now for first step, also parses target side instead of source
enabled parallelization at alignment stage (using --jobs)
tm lines can now be matched to the owner to make replacing just the one you want easier

e.g.,

cat joshua.config | $JOSHUA/scripts/copy-config.pl -tm/glue "new glue file..."
updated copy-config invocation
serious bugfix: weights not added because CONFIG file was closed in loop instead of after loop
Added GHKM ability to the pipeline