We have a WP network (with domain mapping) that was started pre WP 3.5, so it was using ms-files.php and wp-content/blogs.dir/ to store media files. I wanted to remove ms-files.php dependency and after doing some research started the process:
I first tried not moving any files from blogs.dir/#/files to uploads/sites/#, but to setup symlinks for that. Then I had some permissions issues so I just copied everything from blogs.dir/#/files to uploads/sites/#.
Then I cleared the values for upload_path, upload_url_path and fileupload_url on each site.
And finally updated/inserted ms_files_rewriting = 0 in the wp_sitemeta table.
Also added some rewrite rules to the .htaccess file to not have to deal with updating all URLs in DB.
The main blog id in our setup is 2 and not the default which is 1: define('BLOG_ID_CURRENT_SITE', 2);
As far as I know, and based on what I see in wp_upload_dir(), WP uses the root of the uploads folder for the main blog contents and uploads/sites/# for other blogs. So I have copied the content from blogs.dir/2/files to the root of the uploads folder and NOT to uploads/sites/2.
Now here is the issue for media files on the MAIN BLOG: in the back-end, WP loads files from the uploads folder which is fine, but on the front-end it tries to load files from uploads/sites/2 which doesn’t exist and is weird!
PS: I can just add another rewrite rule to have this fixed, but I really want to know what the reason is for /sites/2 being added for the main blog.