Drupal as a simple file manager
Take a look at the IMCE module.

It's a powerful upload manager that requires either CKEditor or IMCE Wysiwyg API bridge to work.

It supports per-user upload directories and space quotas, amongst other useful stuff.

As for the XML-RPC, you should take a look at the Services module.

Regardless of the path you take, you will definitely need to add some custom code and, to help with that (Drupal 7 only) take a look at the FileTransfer class. (related question)