site/files folder
Contains all uploaded files, created either for by the Special:Upload or the Special:Upload Multiple pages.
The files are stored with their name. Uniqueness is not guaranteed. Files with the same name are overwritten. However, if you backup frequently, you may preserve older files, as they are saved in the order of the revision.
If you have many files, do not place them directly in the files folder. Place them in the upload folder and use the Special:Upload Multiple page.
You may prevent direct access to the files using a htaccess File.