When everything is converted, the title page is done, etc. a final check should be done that all the files fit into one single directory which can be moved around without breaking anything (i.e. if there are no absolute links used by accident). If there's a reading rehearsal, it goes into it's own directory, just as the full version does. Any additional files (title page, table of contents, misc. images, ...) should be kept in one directory as well.
All the data can then be delivered via the same ways as the source of the document was received, either electronically or via traditional media, most probably in the form of compressed archive files when using electronical delivery. If there's a written conversion contract, it may specify this further.
If the publisher or project leader requires a conversion report, as was mandatory during the MeDoc project, this report should be included on the media for final delivery as well.
If a media such as CD-ROM is used for delivery, it should contain conversion report, title-page (and any auxiliary files), reading rehearsal and full version each in it's own directory, together with a README file describing which file/directory belongs to what, and (with directories full of HTML files) where the starting file is (if there is no index.html).