For Windows and Linux, you can use Gnotero http://www.cogsci.nl/gnotero to quickly access your PDF attachments without going through the Zotero interface. This isn't quite the same as your curated hierarchical folder structure, but it may cover the same needs.
Maybe a reason to do this is that fact that Mydrive.ch has limited the number of files per folder to 1000 (who says that others wont do the same?). If Zotero would store and sync the pdfs at least in the first level folderstructure this would be really helpful.
Syncing is a separate issue - even if Zotero had a different folder structure the syncing would still work in a similar way. Linked files are not synced, though - I don't quite understand why that's relevant, so maybe I'm not following your point.
Oh I'm sorry... since you adressed the fact that linking a file will be possible by drag and drop in the near future. So i was wondering if the linked files will be synced then as well.
Even if the linking of files would be a solution for this particular issue, the resulting problem that files are not synced would be the next one.
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Or does zotero sync linked files too?
Linked files are not synced, though - I don't quite understand why that's relevant, so maybe I'm not following your point.
Even if the linking of files would be a solution for this particular issue, the resulting problem that files are not synced would be the next one.