Extensions: add a new error type "FATAL_ERROR"

Some errors were reported as warnings because they didn't prevent the
operation from completing (such as failing to remove some paths when
uninstalling).

Change message types for the extensions internal command line program:

- Add "fatal error" to use when an operation fails and exits with a
  non-zero error code.
- Use "error" when an operation fails which doesn't prevent other
  actions from succeeding.
- Use "warn" reporting issues what don't prevent the operation
  from completing but may cause problems.