bump versions of various dependencies
Add bioproject XML and binding generator config

Bindings are generated using JAXB2. Most of the configuration is kept
out of maven and instead can be found in the bindings.xsd file.
Change package code is generated in
Add document chunker class to parse XML
fix missing jars spring, deprecated class use
whitespace change, pom
Fix old JdbcOperations usage
Fix document chunker, can now process package sets

In order to use the unmarshaller, needed to virtually send start
document and start tag for the PackageSet. Otherwise it would choke on
seeing a Package tag, which is not top-level in the schema.
pass packageset attributes correctly
Pass output of chunker to external class
Add preliminary conversion to BioProject
add parsing of simple description properties
Add project relevance and locus tags
Remove unnecessary imports
Add class documentation for domain converter
Use Calendar instances for datetime binding

XMLGregorianCalendar is unnecessary here since we will not use the extra
resolution. Therefore customized the bindings so they have date-time
properties of type Calendar, which is much easier to interface with the
database later.
Add publications from project description
Remove deprecated class use from Mapping loader
Add external links in domain conversion
Return more useful exception when bioproject.xml is not found