When trying to merge /pom.xml on branch R1 to branch R2 git didn't detect 
the merge and tried to put the changes into /pom.xml on R2.  I am guessing 
this is because when it went to merge /pom.xml on R1 to R2 it found a 
/pom.xml on R2 and did not bother to attempt any rename logic.  

On R1 /pom.xml is the webapp's pom.xml file.  On R2 /pom.xml is the parent 
pom.xml file.  It makes no sense to try and merge two different files 

I would be surprised if it was an msysgit issue, but I provide it for 

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