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site_libs/quarto-nav/quarto-nav.js

@@ -274,7 +274,10 @@ window.document.addEventListener("DOMContentLoaded", function () {
     for (let i = 0; i < links.length; i++) {
       if (links[i].href) {
         links[i].dataset.originalHref = links[i].href;
-        links[i].href = links[i].href.replace(/\/index\.html/, "/");
+        // only strip index.html at the end of the path (optionally followed
+        // by a query or fragment) so that files like index.html.md
+        // (alternate-format twins) are left alone (#14667)
+        links[i].href = links[i].href.replace(/\/index\.html(?=[?#]|$)/, "/");
       }
     }