What confirmation options should there be? Here's my thoughts on options:

A. Automatically overwrite the file
B. Keep both files, but append a sequential number on the new file's filename.
C. Do not overwrite; prevent uploading of the file.
D. Prompt the user each time on what they want to do (any of the above 3). Have an overlay dialog that lists each file conflict with 3 small buttons on the right: "overwrite", "keep both", or "skip".
- Or, use a list with check boxes and only one set of buttons, and the user can quickly apply their preferences. The dialog remains on screen until something is applied to all listed conflicts (unless the user clicks cancel, which "skip" is then applied to all remaining items).

First, clarification;
1) filedump allows uploading multiple files at once, hence the need to have a checkbox list to determine what to overwrite
2) the media tag allows direct file upload, which is a direct front-end to the filedump
3) don't worry so much about 'media' tag confirmations if it proves complex, you can do the first half of the issue only if you wish

Do a checkbox list. Not checked means don't overwrite. Checked means overwrite. Only one button. No need for overlays or anything, it is a linear process - can just be an interstital confirmation screen that comes up if a conflict is detected.

I don't feel a need for sequential numbers, too messy for a shared media repository.