fixed network merger to ensure commutatitive ops

fixes #49

Squashed commit of the following:

commit 9a4f6f016be04d5dc94763000f8374a34e7dfa64
Author: Anthony Bargnesi <abargnesi@selventa.com>
Date:   Tue Sep 25 13:53:45 2012 -0400

    fixed proto network merging; updated unit test

    added commutatitive tests for subject-only, statement triples, and
    nested statement documents

    fixes #49

commit 292c68ab2b09c2c8dde0e18301e89fa5d3810d7a
Author: Anthony Bargnesi <abargnesi@selventa.com>
Date:   Mon Sep 24 22:02:39 2012 -0400

    first attempt at a fix to issue #49

    includes unit test for the commutitive property
added find all UUIDs by KAM Node query
removed encryption from framework

includes encryption api, impl, packages, references, and the passphrase
system configuration property

improves phase IV by roughly 2.4% (15 seconds) when tested on the
large corpus

fixes #20
removed commons codec pkg from OSGi imports

work for issue #20
fixed kam node uuid query; @ schema replacements
improved StringColumn.decodeData performance

decodeData was noticably slow using regex pattern matching

switched to checking the length of the trim() function and returning
the "" (empty string) if 0

over 1000000 strings the run-time went from 1500 to 30 milliseconds
do not include null refs when finding by uuid
do not infer ortholog on null kam reference

this should only occur when a kam node was previously collapsed
encode UTF-8 string value before objects insertion
always trim StringColumn's decoded value

a trimmed length of 0 returns the "" string (single instance)
improved parameter quoting

quoting parameters occurred if it contains a non-word character but failed
to check if the parameter matches a reserved keyword

now quoting occurs if a non-word character exists, the parameter matches a
BEL function, or the parameter matches a BEL relationship

refactored quoting of a parameter to BELUtilities
resolver service looks up using equivalences

the resolver service will now use equivalences to match nodes and edges
fix resolver to handle pmod, sub, trunc correctly

pmod, sub, and trunc functions are not counted as parameters and pass
through to the term signature
resolve node query using multiple joins w/ index

added ordinal index to speed up multi-table join for kam node query by
term signature and uuids (1 or more)
BELStatement grammar catches all lexer/parser err

lexer/parser tracks all errors but prevents System.err output

cleaned up BELParser and added javadoc
fixed resolve nodes/edges to handle null namespace
storing human-readable BEL label for each kam node
quote parameters that are bel script keywords
renamed KamSpecies to OrthologizedKam; updated doc
split out orthologize process from kam subclass

orthologize algorithm split out into DefaultOrthologize

OrthologizeKam is created using DefaultOrthologize.orthologize(...)

updated SpeciesKamTest