BilingualRule: include alignment

Instead of hard-coding a null return for getAlignment, include
alignment as a byte [] field. This adds one pointer of overhead
for every rule in a non-packed grammar regardless of whether
alignments are included or not.
HieroFormatReader: read optional alignment field
KBestExtractor: add rule alignment in %d output
Merge pull request #161 from jweese/rule_alignment

Rule alignment
Enable formatter on/off tags
Failed parse now outputs source (instead of empty) string
Bugfix: wrong sign on floor value
Bugfix: OOV list nonterminals now recognized as such

The decoder expects nonterminals to be surrounded by square brackets prior
to being integerized, which was not the case with nonterminals pass in. Now,
they can be passed in either with or without them and the decoder will do
the right thing.
Bugfix in handling of oov-list

Defer converting to ID till after main grammar is loaded.
include alignment for OOV rules
Merge pull request #162 from jweese/rule_alignment

include alignment for OOV rules
Updated README
Refactored derivation-visiting code
New hypergraph format (following @kpu: https://github.com/kpu/lazy)

Use with -output-hypergraph "%d.hg", where "%d" will be replaced with the sentence ID.
Bugfixes in run bundler (fixes #163)
Merge branch 'master' of github.com:joshua-decoder/joshua into devel
Update README to include instruction to run ant devel first.
Merge pull request #164 from chrismattmann/README-update-with-devel

Update README to include instruction to run ant devel first.
Adding Spanish to English readme.
Updated some comments.