[Bioperl-pipeline] Document day

[Xiao Juguang]

Hi guys,

I need to have a day for document, since coding work for pipeline designer
makes me sleepy+headached today.

Meanwhile I should step slow in coding since I have met some problem in the
complexity of the piles of classes.

Here is the one of documents I am writing, to explain the one side of the
complexity of the application, enabled/disabled issue.

I also hope you join in the design early, before I made a big mistake hole.

Juguang.