Hello,
The pre-re and re folder is for you to choose between renewal setting or pre-renewal, for information of renewal change http://ro.doddlercon.com/wiki/index.php?title=Renewal_Changes
Default setting is Renewal, if you want to change it to pre-renewal you will need to edit your source and recompile, http://rathena.org/board/topic/62198-turn-off-renewal-and-make-it-pre-renewal/
If you want to edit players for command, please check this thread http://rathena.org/board/topic/69147-setting-commands-for-normal-players/
Hope it helps, goodluck