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The current latest official 6.x-1.x version of "File (Field) Paths" - 6.x-1.4 - does not properly work with the latest official 6.x-1.x version of the "Comment Upload" module - 6.x-1.0-alpha6, at least under PHP 5.3.x.
With filefield_paths 6.x-1.4 (which is already two and a half years old) I am receiving the error
Parameter 2 to filefield_paths_filefield_paths_process_file() expected to be a reference, value given in /usr/share/drupal6/includes/module.inc on line 497.
and the uploaded file will stay directly under the files directory instead of being moved to the configured target location.
This bug has been fixed on 6 Feb 2012 - thus the latest dev snapshot (6.x-1.4+9-dev) must be used in order to properly work with the "Comment Upload" module.
To avoid relying on a dev snapshot, it would be nice to have a new official 6.x-1.x version (6.x-1.5) released. Thanks.