Basic BLAST XML merging implemented and apparently working:
https://bitbucket.org/peterjc/galaxy-central/changeset/ebf65c0b1e26

This does not currently attempt to remap the iteration
numbers or automatically assigned query names, e.g.
you can have this kind of thing in the middle of the XML
at a merge point:

<Iteration_iter-num>1</Iteration_iter-num>
<Iteration_query-ID>Query_1</Iteration_query-ID>

That isn't a problem for some tools, e.g. my code in
Galaxy to convert BLAST XML to tabular, but I suspect
it could cause trouble elsewhere. If anyone has specific
suggestions for what to test, that would be great.

If this is an issue, then the merge code needs a little
more work to edit these values.

I think the FASTA split code could be reviewed for
inclusion though. Dan - do you want to look at that?
Would a clean branch help?

Peter