added master_xref_id to object_xrefs to fix problems with only one entry in the dependent_xref table. Also new routines added to reset the database to specific points in the xref process

Mention new fetch_all_by_GOTerm_accession() method.

  fetch_all_by_child_term() --> fetch_all_by_descendant_term()
  fetch_by_child_term()     --> fetch_all_by_child_term()

  fetch_all_by_parent_term()    --> fetch_all_by_ancestor_term()
  fetch_by_parent_term()        --> fetch_all_by_parent_term()

  fetch_all_by_child_term() --> fetch_all_by_descendant_term()
  fetch_by_child_term()     --> fetch_all_by_child_term()

  fetch_all_by_parent_term()    --> fetch_all_by_ancestor_term()
  fetch_by_parent_term()        --> fetch_all_by_parent_term()


Also, make accessors read-only.

doc corrected

translation_stable_id, translation_version, peptide_archive_id ought
to be NULL for genes that lack a translation.  This patch fixes these
fields to allow for NULLs.

in the gene_archive table to be NULL.

Properly assign internal IDs to terms when loading 2+ ontologies.

the relation_type_id.  SO has one instance where two terms have two
relations between each other.