Your tool is either not tested well enough since it seems to use your native filesystem and not expect it to be vfat ntfs or the like and barfs on the lineendings or symbolic links. Or you did something wrong with any git repo checkout like using native lineendings or unpacking things by hand instead of letting the script/tool do it. Did you move part of the stuff from your other computer to this one?
I: Done! Enjoy! I: Cleaning up...