Don't fail publishing on overwrite, but issue a warning.

Workaround for #1156.

* Creates a new FileRepository that will stil allow local files
  to be transfered if overwrite is true (non-snapshot module),
  but will issue a warning about deprecated behavior.
* Ensure warning is long enough to annoy people into asking
  what it's about.

Review by @dansanduleac (if you have time)