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Adding index.php file
or htaccess Options -Indexes
What was the size of the files? If they're heavier than 10 MB, they won't be uploaded.
Have you checked that all of there permission's for the files are the same as if any of them are set to write only you won't be able to see them!
What's so important about the directory listing? What are you actually trying to do?
is infinityfree limit file in every subfolder in ftp ??