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Batch processing files in separate directories under Windows?

I'm trying to write a script that will do the following in batch mode:

* Take a list of files in two separate directories.

* Take the first file in one directory, the first file in the second directory, and then create a layer in a new image that is the difference of these two images.

* Do the same thing for the second file in each directory. This layer will be the second layer in the new image.

* Do the same thing for the third file, and so on until all of the files are completed.

* Save the new layered file down as a gif.

All of the original files are jpgs, and are all the same dimensions, so no resizing will have to be done.

I have a script on a separate computer (I'll type it in later for your perusal) that is giving me an error message before it even gets into main part of the script. My question is that because I'm running this script on a Windows box, are the slashes in the directory names going to cause a problem? I've written and run other batch scripts before, but this is the first time that the files I'm editing are in two separate directories. (Some of the file names are the same, which is why they need to be kept in separate directories.)

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