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When passed "#internal-anchor" on a page other than the top-level index, the url filter returns a relative path to the top-level index.
Like, if I have a page about.md and the page.url is about/; if I pass "#internal-anchor" to the url filter, I get ../#internal-anchor.
The url filter should not modify those URLs that are internal to the current page.
(I suffer from this problem when using the material theme; in 3.0.4, in the "Skip to content" link, it passes a toc item's url to the url filter, which breaks it on every page except the top-level index. HTMLProofer complains about the broken link.)
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This has gone unnoticed because the builtin themes did not pass TOC URLs through the url filter. As all TOC URLs have only ever been for the current page, there was no need to do so. However, with #1594 the readthedocs theme now offers the option to include the TOC for all pages in the nav. Therefore, this could be a problem for that theme as well.