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Using a GUI file managers you can merge directories (cut and paste). This command roughly does the same (it doesn't ask for confirmation (no problem for me) and it doesn't clean up the empty SRC directories (no problem, trivial).
probably does the same:
cp -l SRC TARGET; rm -rf SRC
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Have a look at rsync, does this and much more.
Eg: (NB: the trailing '/' characters are important)
rsync -va --remove-source-files SRC/ TARGET/
Forgot -r flag:
cp -lr SRC TARGET; rm -rf SRC
@lingo: true, I never looked into the rsync's hard-link options (particularily want to use hardlinks to avoid the overhead of physically copying the data)
The following command should do it
rsync -a --link-dest=SRC SRC/ TARGET/and, of course --remove-source-files. Nice, did't know about that one either