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How can I merge two folders with the same or different names with subdirectories, using shell script or terminal. Also, if there is a file with the same name, then it should skip.

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What operating system are you on? Is there anything you've already tried? –  slhck May 20 '13 at 13:38
I am using Ubuntu. I want to merge using shell script or through terminal. –  sonu May 20 '13 at 15:37
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To merge "dir2" into "dir1," I would expect the following to do what you want:

cp -nr dir2/* dir1/

The -r switch means copy recursively, and the -n switch means don't overwrite existing files (i.e., skip files with the same name).

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