Overall structuring of the site feels awkward
For starters, the sidebar tree feels a bit too deeply nested; as a "quick fix" I'd probably make Administration/Development/Contributing their own toplevels and lift their children up to the top of the sidebar. Some of the categorization would be better suited as inline headers in the sidebar instead of another level of nesting.
artist rendition of a straightforward but fruitful improvmeent to the sidebar structure
the category pages feel a bit Unstructured as just a plain but large list of their contents; they could have a similar treatment to the sidebar and have inline headers
artist rendition of improvement:
Have you taken a look at https://github.com/PaperMC/docs/pull/346 yet? Most recent change on that PR is deployed here
cool, that's how i would start untangling the site's structure