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You can add 'foreign files' e.g. FLV, MP3, XLS, EXE... via Add Books->Add files to selected book records (Shift/A), you may need to adjust the file type selection in the open filke diialogue.
Calibre wont process the files in any way, but it will record their existence and keep them in the folder if the books are moved to another library, or the author or title is changed etc. You can open them in the designated program via the Book Details panel, or the Open With plugin etc, or in the Edit Metadata dialogue
But you can only have one file of each type. I get around this limitation by keeping 'foreign files' in a single 7z archive when there's more than one of any type.
Can't help you with the other issue.
BR
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