Merge pull request #62 from zgzn/sbol2

First major core 2 class refactoring as a result of the decisions made at COMBINE this year.
Delete .project
Delete org.eclipse.core.resources.prefs
Delete org.eclipse.m2e.core.prefs
Merge pull request #63 from zgzn/sbol2

Updated SBOLDocument Class
Merge pull request #64 from zgzn/sbol2

Removed type List for two field variables.
no testing file generated
Merge remote-tracking branch 'origin/sbol2' into sbol2
Merge pull request #65 from zgzn/sbol2

Added getters and setters for field variables.
Merge pull request #66 from zgzn/sbol2

Renamed RefersTo to MapsTo.
Brought in new sbol-data reference to resolve DocumentRoot()
declaration. NamedProperty() is now called with one parameter instead of
two.
recommiting and pushing last changes for DocumentRoot() and
NamedProperty()
Merge branch 'sbol2' of https://github.com/SynBioDex/libSBOLj.git into sbol2
Working test serialization for Module
Merge pull request #67 from zgzn/sbol2

Changed reference from actual objects to their URIs for all hollow
Implemented a working set for retreiving data for component and module.
Merge branch 'sbol2' of https://github.com/SynBioDex/libSBOLj.git into
sbol2

Conflicts:
	core2/src/main/java/org/sbolstandard/core2/SBOLDocument.java
brought in new changes made on SbolDocument.java and merged with
SbolWriter.java. Errors were resolved but sample data needs to be more
detailed tested.
Delete .project

Removed .project for "brought in new changes made on SbolDocument.java and merged with
SbolWriter.java. Errors were resolved but sample data needs to be more
detailed tested." Committed on 10/22/2014
Delete org.eclipse.core.resources.prefs

Removed  .settings / org.eclipse.core.resources.prefs for "brought in new changes made on SbolDocument.java and merged with
SbolWriter.java. Errors were resolved but sample data needs to be more
detailed tested." Committed on 10/22/2014