> I know the general versioning problem is address through the tool-shed 
> mechanism, but for the remaining core wrappers, can maintainersplease update 
> wrapper version numbers when making changes?

Not bumping wrapper versions is an oversight, not deliberate.
 
> 
> For this wrapper set, how would you advise us to support both?

Fortunately, I refactored the Cuffdiff wrapper recently and correctly bumped 
the tool version:

https://bitbucket.org/galaxy/galaxy-central/commits/6a32d26aefc758cf576e0b753c2626ac56005c18

You can either pull this changeset manually or wait until the next distribution 
in early October to get the changeset.

Best,
J.
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