EDIT

preparing for hibernate-c3p0 & commenting out all System.err.println

minor

new test for the delete method of TaxonNameDao

#1390

Altered ReferringObjectMetadataFactoryImpl to exclude bidirectional relationships where the replaced entity is the "owner" of the related entity (i.e. the relationship is mapped by @OneToMany & mappedBy != null) since those kind of relationships don't make sense in the context of a global replace method.

Updated ICdmEntityDao replace(T x, T y) and refresh(T t, LockMode lockMode, List propertyPaths) and added methods to IAnnotationDao

Added public T replace(T x, T y) to ICdmEntityDao, implementation and tests

Added an IIdentificationKeyDao to query across all identification key types

Refactored free text search to re-use the same code for all identifiable entities. Switched to StandardAnalyzer to include indexing of numbers. Removed redundant code from taxonDao.delete() method (as included entities deleted using hibernate's cascade method)