The situation is - we want to incorporate a large, existing site with a lot of legacy file download links etc (bookmarked and hard-linked to from all over the place) into a Drupal document management system.
Sorry, Apache mod-rewrites are out of the question, and they'd totally confuse the later editors.
I've had some success with what I need to do to re-attach files to their appropriate Drupal nodes, but the first way of doing that for a site admin was to set the "File Directory" to "." - effectively allowing all the sites files to be available for attachment, and to allow admins to upload to various places. (I also built a 'save-as' plugin).
I've so far avoided making my own table or my own file-save methods by beating the existing upload.module into submission, (by lying to it, not by patching it) but I don't want to leave the 'files' directory as '.'
I don't want to build another alternative filemanager, like so many others have tried, I want to remain close to core.
I'm looking into (eventually) setting different base 'files' directories by roles, or by page type, or by alias path, (probably a bad idea) but all of them would like to know what the true path of a file is.
Currently, the 'files' table stores relative paths in the database, and these are rendered with the active file directory plugged on the front of it. This is why changing the files directory on a live site causes death.