Addressed more comments for adding word alignment to rules.

-- added some TODOs to indicate that rules may be better built
on the fly during extraction (plus added issue on github)
-- added a unit test for extraction
-- added a commented example code on how to print word alignments
for rules in retrieval.
-- timing experiments for the full WMT13 RU-EN set:
            without alignment | with alignment
extraction  96m               | 106m
s2t         12m               | 12m
t2s         14m               | 13m
merge       28m               | 41m
retrieval   10m45s            | 11m11s