inmemory vs. DB backed ontologies

[bolerio]

Currently, there is a single ontology manager that handles both HGDB stored ontologies and the ones loaded from file in memory. This is a bit problematic because it unnecessarily pollutes the DB with temporary stuff. For example, GC is forbidden because of that interference:

    // if we have an in memory ontology that has been modified and was unsaved, we
    // can't do garbage collection because some of the entities might get deleted?
    // not sure why this was done....perhaps we should make the plugin deal 
    // completely independently with inmemory ontologies and HGDB-backed ones so
    // that loading in memory doesn't have any impact on the DB at all. 

so yeah, the idea would be to segregate two ontologies managers, but that should be transparent to protege.