I currently edit a lot at Wikia and I frequently find that I cannot use the General fixes functionality because it adds the Uncategorised, Orphan and Deadend and these templates aren't used there.
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If you turn off the "Auto tag" option this should stop any of these templates being added. Does that work for you?
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It does stop adding them, but it stops adding others that we would like to use as well. I guess for this it would be nice if the Tagger could be modified like Alerts. If a tab was added with the various tagging functions, then the user could select which ones they wanted to use.
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Being able to select individual templates to be added would be the only way to do this, since Wikia is not a single cohesive template environment. Rather, each Wikia wiki maintains its own collection of templates, and so different communities have different use cases.
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That's true in general. I don't think any Wikia Projects are using these three though and if they are they are the exception and not the rule. That even applies to some WMF projects to though. But I do agree it would be a great improvement, if the user could designate which tags they want to work with like AWB currently allows for Alerts.