Merge pull request #157 from jganitkevitch/devel

Packer and tokenization updates
Decoder now searches for feature functions in src/joshua/decoder/ff/

This allows you to add a new feature function without adding a corresponding
if statement to Decoder.java to load it. Currently only works for features that
don't take any arguments, but could easily be generalized a/c to the interface
(which isn't currently used very consistently)
Added RuleShape feature
Removed line preventing compilation
Fixed to take String[] args
Added alignment to default extracted features
Pipeline now handles mixed dense and sparse features in any grammar

This required extending the EncoderConfiguration to print out feature names,
and then generalizing the pipeline to use those feature names in the initial
config files that it generates for tuning. Default values for everything are 1;
it might be worthwhile allowing sparse features to be initialized to 0, either
hard-coded or as an option.
Merge pull request #158 from jganitkevitch/devel

Mixed mode packing now 0-indexes unlabeled dense features.
Modified Hiero format reader to permit alignments in grammar file
Fixed interpretation and naming of sparse and dense features
Fixed printing of feature names
Added compatibility for old packed grammar format
Bugfix: shadow declaration in catch
Bugfix, was pulling number of features from feature map before generating it.