The temporary solution for uploading source files to our journal is this:
We don't use the extensive copyediting procedure, since most of this is done in the review process. So I abused the author step of copyediting for uploading of source files, because this is the convenient point in the paper processing workflow that allows the upload of files by the author.
What I do is, after the review process is finished, I (in the role of the editor) start and complete the first phase of copyediting without actually doing anything and then initiate the author step of copyediting, but I skip email, and send the author a custom email, where I write instructions for uploading the original files - I advise the author to pack everything in one ZIP file and upload this in the Author part of copyediting process. The editor can then download this file and upload it to the Layout editing step, where it can be accessed by the Layout editor. Our authors use Word or LaTeX to prepare text, so we need the source files to build a print version, as well as figures in print resolution.
The workflow using supplementary files is not a good option for us, since the papers in our journal usually contain a lot of figures (http://www.ias-iss.org/ojs/IAS/
) and the authors could get confused with all the options that are available for supplementary files. Plus, we occasionally need the actual supplementary material, so the workflow could get very confused.
I propose that an additional (optional) section would be added in the Editing step for uploading of original files - the interface would be made from an upload box, a file list, and a button to delete a file if it is uploaded by mistake. The files would ideally be uploaded to a subdirectory in the article directory and retain their original name, eg. Figure-1.tif, Figure-2.eps, etc. so that the Layout editor would know where to put the figures in the text.