FTP files directly to Media Library wp-content\uploads

I would suggest using WP CLI for that. It’s the (in)official WordPress command line tool, like Drush for Drupal or the Symfony2 Console Component.

Use the media command to handle your (future) attachments:

wp media import <file> [--option=value*] 

* Take a look at the docs or the CLI help tool to see what options you got.

wp media import produces WordPress attachment post types from plain files, therefore letting them appear as uploads in the WP media library.

Examples from the docs.

# Import all jpgs in the current user's "Pictures" directory, not attached to any post
wp media import ~/Pictures/**\/*.jpg

# Import a local image and set it to be the post thumbnail for a post
wp media import ~/Downloads/image.png --post_id=123 --title="A downloaded picture" --featured_image

# Import an image from the web
wp media import http://s.wordpress.org/style/images/wp-header-logo.png --title="The WordPress logo" --alt="Semantic personal publishing"

(current state of code base while writing this question – later readers, read the docs on the official site)