As for merging data with pointless/aimless, all you need to do is this:
echo "choose spacegroup P212121" | pointless XDSIN XDS_ASCII.HKL hklout pointless.mtz | tee pointless.log
echo "resolution 2.5" | aimless hklin pointless.mtz hklout aimless.mtz | tee aimless.log
echo "nres 999" | truncate hklin aimless.mtz hklout merged.mtz | tee truncate.log

Modifying them, of course, to reflect the space group, resolution cutoff, and molecular weight you think are appropriate. 

I suppose I could write a little jiffy for this?  
But I'm still trying to determine in the XDS->AIMLESS->TRUNCATE route is better or worse than the XDS->XSCALE->XDSCONV route. 
 The former is certainly slower.  I have seen AIMLESS jobs take 11 hours where XSCALE is done in 2 minutes. 
 Right now, I have "xds2mtz.com", which is a jiffy for the latter that takes command-line arguments of space group, 
resolution, etc.  But still, of course, requires XDS licensing.