what if you start to upload some directories, then you stop for a while,
and while you stop some directories are moved to other places in the
ftp.

When you start again, if you try :
mirror -R directory[c-z]* .
then it will send the contents of these directories to the current
directory, which is not what you want...
and 
mirror -R .
will upload everything again (this time with every file in its own
directory).

So is there a simple solution, other than asking the admin not to move
the files before everything is finished ? ;-)

put / mput does not work neither, it's for files, not for directories.

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