Added ErrorLog for collecting and processing SemSimErrors.
Eliminated the dependency semsim.reading.MMLreader class had on its own
subclass, MMLreader2. Renamed MMLreader to MMLParser and changed its
return type to Document and removed all references to SemSimModel.
MMLreader2 is now MMLreader and is no longer a subclass of MMLParser.
Added static method to SemGenError for displaying errors from SemSim.

Added class PublishingMetadata.
Added abstract class BioModelReader as a parent class for all readers.
Moved double:SemSimVersion to SemSimLibrary and changed necessary
references.