Check when copying a directory finished

Hi all!
I've got an application that scans a certain directory permanently for new directories copied in it. When a new directory is found it starts a thread to process its contents. There is a pause between each check of one second, so moving the directory intendet to process works fine, since only a reference has to be changed, which goes pretty fast.
Ok, fine so far. But i do need to physically copy directories too (program will run on servers and be fed by clients), but if the program encounters a new directory (whether its contents are already there or not) it immediately starts to process the content, whis is error prone.
Now is there a java native, multiplatform solution to check if such a copying proces is finished?
I have some solutions to bypass that problem in mind, but such a check seems to be the most elegant and comfortable way.
Thx in advance

you can copy the directory in to one directory in the same drive and then move the copy to the "inbox" of your application.
By the way how this copying is done
if that is done using a progam (which you can modify the source) you can make it send it some signel to your processing program with the name of the folder that is being copied. so toyr processing checking program can ignotre the folder untile another mesag is received to remove th folder from its exclude list.

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