The information architecture of the documentation is now a bit more organized! 
On the sidebar navigation tree:
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The pages under Your repositories now have only to do with “read-only” use cases, while all pages with instructions on how to make changes to the configurations of the repositories are now under the section Configuring your repositories
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The order of the pages now follows a more natural sequence that matches the one on the Codacy UI
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Instructions on how to set up coverage are now under the section Related tools, where we’re grouping all “local analysis” tools before performing further improvements
This simplifies the amount of information that is mostly aimed at personas with different permission levels and hopefully improves the findability of pages containing related information. 
If you’re curious you can check more details about all the changes on this pull request. 
Let us know what you think, and what further improvements you would like to see first on the Codacy documentation.