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In my case, this is exactly: I'm using media_youtube in a field. In this, I've enabled upload image, or embed youtube video. When upload a youtube video, the file display completely broken, because of moving files.
These should be solutions:
1. Only process file, it has own extension.
It works with embed video in my case, but the question is: Uploaded files without extension always need to skip ffp process?
2. Add field to ffp administration, where user can edit the exceptions of ffp process, eg can set some file filemime.
3. Other modules what provides this type if files need to use hook_filefield_paths_process_file() to set $file['new'] always false.