It looks like the .htaccess file is not updated if there is no permalink structure specified – even if there is a category base, or rules added by plugins.
If I go to the permalinks page, and change the category base and leave the permalink structure blank; when I click the save button, the message indicating the permalinks were updated displays, but the .htaccess file remains unchanged.
I’m not sure if this is broken, or whether it was intended to behave like this (i.e. only update permalinks when there is permalink structure specified).
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