Upload.module
- Fixing a bug caused by the PHP5 patches.
Beware: PHP4's array_merge() will silently accept objects and convert them to arrays. We should not depend on this behaviour in the future.

File.inc / file-using modules:
- Removing the constant FILE_SEPARATOR: forward slashes work fine on Windows, and it was being used incorrectly as an URL separator sometimes.
- Adding @ to mkdir and chmod to supress ugly PHP errors. They are already reported with drupal_set_message().
- Fixing default for variable 'file_directory_temp'.
- Clarifying the help tip for 'file_directory_temp' in admin > settings.