[Bioperl-pipeline] xml dir housekeeping -- No hardcoding

[Elia Stupka]

> It is hard to define the standard of whether it is hardcoding or not.

Actually not too hard. If your software works for somebody (or fails
gracefully) on a new virgin computer on the other side of the world, then
nothing is hardcoded. If your software fails misteriously pointing to a
resource not available on your machine, then there is hardcoding.

Ideally the software should never *fail*, if something is missing it
should identify it and tell you kindly about it, until all works....

;)

Elia

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