Added tool to convert Moses phrase table to Joshua grammar (for packing)
Added printing of alignments in phrase-based output
BUGFIX: The OOV penalty was not contributing to the rule's estimated cost

This is important because the estimated cost is used to sort rules during cube pruning. OOV rules were at the top prior to this.
BUGFIX: indexes are positions between words
Commented out a bunch of crap
BUGFIX: invalid use of "i", fixed Hypothesis equals()

Was using HGNode's "i" parameter to keep track of the beginning of a phrase, but this isn't valid, because i is not part of the DP state. Corrected this by computing i where needed by subtracting off the number of words on the rule's source side.

Also (important) fixed the Hypothesis equals() code to compare DP states