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When a page needs to be changed in order to refresh all kinds of relations, touch.py can do the work. This program updates a record without making any changes. Running touchall.py will not create entries on the "recent changes". Technically, what it does is take each page and save it, without making any changes (null edit), thus refreshing the relations with categories and other relations.
start: The default is to go through all pages from Special:Allpages in order. This may however be done spread out over various runs. If one wants to continue, give the argument "-start:page!" with page the last page of which you know it has been done. The bot will then do the pages coming after that.