removed dependence on hadoop
fixed whitespace
speeded up exact filtering by first chaining to fast filtering
added top level glue rules (
 [S,1] 
) glue rules to glue grammar extractor
Checked off TODO.
Merge branch 'master' of https://github.com/joshua-decoder/thrax into compact

Conflicts:
	src/edu/jhu/thrax/util/CreateGlueGrammar.java
	src/edu/jhu/thrax/util/TestSetFilter.java
Fixed warnings and formatting.
Fixes to alignment and lexical probability features, overall grammar extraction.
Fixes to p(e|f), p(f|e), annotation-level features. Ported simple features to integer-based representation.
Fixed lexical probabilities, p(LHS|*) features.