If you use Leanpub's workflow to generate your book, but you also want to upload a custom PDF file you have created using another workflow, here are the instructions:
Make a folder called "custom" at the top level of the Dropbox folder for your book (it should be a sibling to your manuscript folder).
Put a file in there called
SLUGis the name of your book in its URL. (For example, if we were doing this with the Leanpub manual https://leanpub.com/manual, we would have to name the file
If you have also created a sample PDF, put the file in the "custom" folder and rename it to
Re-publish your book.
We will then generate the EPUB and MOBI files for your book, and also use
the PDF file you have provided.
For those who are curious about why someone would want to do this: PDFs give you a lot more control over formatting than the EPUB and MOBI formats do.