1. Is it possible to copy a file to a usb drive and simultaneously fragment the file?
Not with MyFragmenter, no. MyFragmenter cannot copy files between volumes. It fragments files with system calls from the Microsoft defragmentation API, and this API can only move files inside a volume. You will first have to copy the file to the usb drive, and then use MyFragmenter to fragment it.
2. Is it possible to fragment multiple files at the same time?
Yes. Simply specify all the filenames on the commandline. Please note that Windows has a limit on the length of the commandline, depending on the Windows version.
3. When fragmenting a file, what happens with the clusters which used to be occupied by the file? Does it overwrite the old clusters?
The old clusters are not overwritten. They are discarded and marked "free", similar to when a file is deleted.
4. How do MyFragment determine where to put the file parts? Is it a random or a fixed location?
MyFragmenter looks for the largest gap on disk and puts the part bang in the middle. This is repeated for all the parts.
5. How do MyFragment determine what part of a file should be moved? Fixed or random?
The entire file is moved, one part after another starting at the beginning of the file.
6. Is it possible to view the source code of MyFragment?
7. Is it possible to edit or add code if needed?
Sorry. The sources of MyDefrag (and MyFragmenter) are not public domain, they are copyrighted and only available for a hefty license fee.