When it comes to resolving the "problem", you've got three options, I guess:

1) Leave it like it is and keep on working
2) Force a rewrite of history onto the github master branch. This will 
create problems for anyone who have already cloned with the latest changes
3) Abandon the master branch and continue developing in another branch. 

An idea of the cause: This CRLF 
problem: http://stackoverflow.com/questions/3133163/ugly-git-merge-problem

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