changes needed in cobra to support the coreos/pflags

Because cobra was written with pflags in mind, changing pflags makes it necessary to change cobra. The strip flags function works on the POSIX style of flags. I found that instead of rewriting that function to support the much wider range of flags accepted now, it would be much easier and quicker to add a reformatArgs() function which would take in arguments in the original goflags style and convert them to the style that pflags expects. 

Major changes to review: reformatArgs(), getAllBooleanFlags() 
newline cleanup