The template documentation for en:Template:Main instructs editors to use en:Template:Cat main instead within the Category namespace (namespace 14). In spite of that, currently there are 8,000+ instances of {{Main}} in the Category namespace; see e.g., en:Category:Algorithms. I am requesting that AWB, as one of its ongoing general fixes, replace {{Main}} with {{Cat main}} when it detects {{Main}} in the Category namespace. For more information, see https://en.wikipedia.org/wiki/Template_talk:Main#Category_namespace. Thank you.
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This sounds like a very straightforward single-run job to me, though I echo the last comment in the linked discussion in asking why categories need special wording separate from other pages.
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A single run would fix the 8,000+ current transclusions, but new ones would start to accumulate over time. Regarding the larger question of why categories need a special hatnote, I have requested input from more involved editors at en:Template talk:Cat main and en:Wikipedia talk:Categorization, and I will post here again once a satisfactory answer becomes apparent.
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Even with a slow trickle of new pages, this is a very clearly defined job that shouldn't need any sort of editor judgement; therefore it seems to me that an occasionally-run bot (or even an occasional manual run) would be more suitable than an addition to genfixes.