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You can create simple a simple batch file to handle this for you. It would look something like this:
md 0001
md 0002
md 0003
move 0001*.jpg 0001
move 0002*.jpg 0002
move 0003*.jpg 0003
Then just drop the batch file in the same directory as all the pics, and launch it. It will create any subdirectories right in the main directory, and move the named files to their respective subdirectory.
This of course is only using 3 directories as an example, but I'm sure you get the point.
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