purpose of this repo

[carandraug]

The purpose of this repo is not clear. Can it be removed?

[cjfields]

@carandraug Because this is an open source project I wouldn't remove it, but mark it as deprecated.

[cjfields]

...Saying that, it looks like pretty large chunks of bioperl-dev have been moved to core/run by Mark Jensen. Added a deprecation notice to make this more clear.