Changes to Merge-o-matic: Merges from trees with patches unapplied

[Julian Andres Klode]

Hi,

Currently, MoM generates merges with patches applied, meaning that the 
resulting merge is often useless because upstream files where changed by 
patches, but the patches not pushed in quilt (and other stuff). I 
usually worked around this by extracting the Debian version, and copying 
debian/ over from the tree MoM generated.

An hour ago, cjwatson rolled out my change to make MoM create merges 
using trees where patches are not applied. This should fix the problem, 
but there might be other issues, so please watch out.

MoM also generates larger graphs since yesterday thanks to tsimonq2.

Let's hope we did not break stuff :)

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