Fix variable shadowing.
Rename MetadataInterface to Metadata, add MetadataFactory, move init code into constructors, update references.
Merge pull request #78 from SeqWare/feature/refactor-metadata

Feature/refactor metadata
Merge branch 'develop' into feature/SEQWARE-616_review_and_test_metadata_tools

Conflicts:
	seqware-common/src/main/java/net/sourceforge/seqware/common/metadata/MetadataInterface.java