fix footer to merge references and footnotes from all chapters into one list

app/src/components/Footer.astro

@@ -129,36 +129,94 @@ const { citationText, bibtex, licence, doi } = Astro.props as Props;
       // Prevent multiple runs
       if (footer.dataset.processed === "true") return false;
 
-      const findFirstOutsideFooter = (selectors) => {
-        // Try contentRoot first, then document.body
-        const searchRoots = [contentRoot, document.body].filter(Boolean);
+      const refSelectors = [
+        "#bibliography-references-list",
+        "[data-bibliography-block]",
+        "#references",
+        "#refs",
+        ".references",
+        ".bibliography",
+      ];
 
+      // Find ALL top-level reference/footnote sections (each chapter generates its own).
+      // Filters out descendants to avoid matching both a container and its inner list.
+      const findAllOutsideFooter = (selectors) => {
+        const found = [];
+        const searchRoots = [contentRoot, document.body].filter(Boolean);
         for (const root of searchRoots) {
           for (const sel of selectors) {
-            const el = root.querySelector(sel);
-            if (el && !footer.contains(el)) return el;
+            root.querySelectorAll(sel).forEach((el) => {
+              if (!footer.contains(el) && !found.includes(el)) found.push(el);
+            });
           }
         }
-        return null;
+        // Remove any element that is a descendant of another element in the list
+        return found.filter(
+          (el) => !found.some((other) => other !== el && other.contains(el)),
+        );
       };
 
-      const referencesEl = findFirstOutsideFooter([
-        "#bibliography-references-list",
-        "[data-bibliography-block]",
-        "#references",
-        "#refs",
-        ".references",
-        ".bibliography",
-      ]);
+      const allRefsEls = findAllOutsideFooter(refSelectors);
+
+      // Merge all reference sections into the first one, deduplicating by id
+      let referencesEl = null;
+      if (allRefsEls.length > 0) {
+        referencesEl = allRefsEls[0];
+        if (allRefsEls.length > 1) {
+          // Collect existing ids from the first section
+          const seenIds = new Set();
+          referencesEl.querySelectorAll("li[id]").forEach((li) => seenIds.add(li.id));
+          // Find or create the <ol> in the first section
+          let targetOl = referencesEl.querySelector("ol");
+          if (!targetOl) {
+            targetOl = document.createElement("ol");
+            targetOl.className = "references";
+            referencesEl.appendChild(targetOl);
+          }
+          // Merge entries from remaining sections
+          for (let i = 1; i < allRefsEls.length; i++) {
+            allRefsEls[i].querySelectorAll("li").forEach((li) => {
+              if (!li.id || !seenIds.has(li.id)) {
+                if (li.id) seenIds.add(li.id);
+                targetOl.appendChild(li);
+              }
+            });
+            allRefsEls[i].remove();
+          }
+        }
+      }
 
-      // Try multiple selectors for footnotes
-      const footnotesEl = findFirstOutsideFooter([
+      // Merge all footnote sections the same way
+      const allFootnoteEls = findAllOutsideFooter([
         "[data-built-footnotes]",
         ".footnotes",
         "section.footnotes",
         "div.footnotes",
       ]);
 
+      let footnotesEl = null;
+      if (allFootnoteEls.length > 0) {
+        footnotesEl = allFootnoteEls[0];
+        if (allFootnoteEls.length > 1) {
+          const seenIds = new Set();
+          footnotesEl.querySelectorAll("li[id]").forEach((li) => seenIds.add(li.id));
+          let targetOl = footnotesEl.querySelector("ol");
+          if (!targetOl) {
+            targetOl = document.createElement("ol");
+            footnotesEl.appendChild(targetOl);
+          }
+          for (let i = 1; i < allFootnoteEls.length; i++) {
+            allFootnoteEls[i].querySelectorAll("li").forEach((li) => {
+              if (!li.id || !seenIds.has(li.id)) {
+                if (li.id) seenIds.add(li.id);
+                targetOl.appendChild(li);
+              }
+            });
+            allFootnoteEls[i].remove();
+          }
+        }
+      }
+
       const movedRefs = moveIntoFooter(referencesEl, "References");
       const movedNotes = moveIntoFooter(footnotesEl, "Footnotes");