[Bioperl-pipeline] better re-run management

[Elia Stupka]

> if we plan to change it around, not sure where the logic about checking which 
> analyses are completed etc should go into, i.e, Xml2DB or Pipelinemanager.

? PipelineManager, only the pipeline manager can "see" that an analysis is
finished (just like when it's checking for WAIT_FOR_ALL) and update the
table. Then Xml2DB will have to handle it when it is *writing* to the
database

Elia

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