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[Bioc-devel] whitespace or or end of line format conflict in git merge

While resolving conflicts according to this protocol
https://master.bioconductor.org/developers/how-to/git/resolve-conflicts/
I ran into a quite a number of seeming duplications of the file content
between HEAD and upstream/master. It looks like either some sort of
whitespace or end of line formatting issue.
E.g.
<<<<<<< HEAD
BiocGenerics:::testPackage("MSnID")
=======
BiocGenerics:::testPackage("MSnID")
What is the recommended way to avoid all this trouble?
Thanks,
Vlad