[Bioperl-pipeline] xml dir housekeeping

[Elia Stupka]

> is confusing as to which works and which doesn't. I would like to 
> partition the xmls
> into working ones and under-dev ones. By working I mean they should 
> have a .t
> file and documentation on how to use the pipeline in the xml itself.

I totally agree to keep .t files, and splitting dev and non-dev keeps 
us working actively yet clean...

> On writing pipeline tests, pipeline tests should  be file based, 
> meaning it doesn't assume the availability of biosql or ensembl or 
> other schema. Also no hardcoding.  Within the xml, one can add the 
> various adaptors and stuff but commented out for testing purposes.

Juguang, if any of this is not clear please let us know, so that we 
make sure any of your XMLs are up to speed.

Elia