For the purposes of production, a complete INDD (InDesign) folder, for use by an eBook service company will have contained inside it:

•a folder for "Document fonts," with the fonts contained therein;

•a folder for "Links," with any images, charts, etc., contained within;

•and, the .idml, a file that allows users of other versions of InDesign to use the file;

•.indd file, and

•the final .pdf file(s).

•Some INDD package folders come with the standard instructions for the printer.  (Not needed, but it can be useful to us for font-checking).  

We ask for the PDF file as well because that's a QA (Quality Assurance) measure—it's how we double-check that we have everything.  We output a PDF from the INDD folder, and check it against the PDF file that you send us. If our output looks odd (say, a different font shows up), then we have an instant clue that the folder has something missing.  It's a quality-assurance checking mechanism to ensure we get everything right for your book.

How To Package an InDesign File for use by a Service Bureau/Printer:

 

You can watch this short Adobe video on "how to package your InDesign file for handoff to a service provider" here on Adobe's Help Center. https://helpx.adobe.com/indesign/how-to/indesign-package-files-for-handoff.html