First attempt at separating out domain provider
Remove breakpoints
Move dependency on annotation build out of diagram object

The MutationDiagram object now uses the DomainProvider
API to get the domains.  The command creates the
DomainProvider object and passes it to the MutationDiagram
object.  This way we can write another command that creates
a different type of DomainProvider that doesn't use
ImportedAnnotationBuild
Merge branch 'updated' into gb_master