runPearMerger on already merged PEARs

[Jens Grivolla]

It seems that runPearMerger.sh does not correctly adjust the paths when 
the input PEARs are already a merge.

On first run `runPearMerger.sh ae1.pear ae2.pear -n ae12` the paths to 
resources get adjusted from $main_root/X to $main_root/ae1/X or 
$main_root/ae2/X respectively.

However, on subsequent `runPearMerger.sh ae12.pear ae3.pear -n ae123` 
only the top level paths appear to get adjusted.

Should I file an issue, or is that a known and accepted limitation of 
PearMerger?

Thanks,
Jens