You can use cp -b option to take a backup of each existing destination file/directory before overwriting with the source file/directory.
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mkdir mydir1 mydir2 ## create some files and directory echo "one" > mydir1/myfile1 echo "two" > mydir2/myfile1 cp -b mydir1/myfile1 mydir2 ## creates a backup (myfile1~) of myfile1 before overwriting cat mydir2/myfile1~ ## returns two cat mydir2/myfile1 ## returns one rm -r my* |