diff --git a/make-pdf/src/print-css.ts b/make-pdf/src/print-css.ts
index bf6f862bdc..3cc525870f 100644
--- a/make-pdf/src/print-css.ts
+++ b/make-pdf/src/print-css.ts
@@ -329,6 +329,16 @@ function inlineRules(): string {
     `}`,
     `strong { font-weight: 700; }`,
     `em { font-style: italic; }`,
+    // APA-style hanging indent (0.5in) for reference-list entries. Scoped to
+    // .references so ordinary body paragraphs are untouched. wrapped by
+    // render.ts's wrapReferencesSection() around the content following an
+    // <h1>References</h1> heading.
+    `.references p {`,
+    `  margin: 0 0 11pt;`,
+    `  padding-left: 0.5in;`,
+    `  text-indent: -0.5in;`,
+    `}`,
+    `.references p:first-child { margin-top: 0; }`,
   ].join("\n");
 }
 
diff --git a/make-pdf/src/render.ts b/make-pdf/src/render.ts
index 514fbbc89e..9c35a972eb 100644
--- a/make-pdf/src/render.ts
+++ b/make-pdf/src/render.ts
@@ -87,8 +87,13 @@ export function render(opts: RenderOptions): RenderResult {
   // 4. Smartypants (code-safe)
   const typographicHtml = smartypants(decoded);
 
+  // 4.5. Custom cover extraction (see extractCustomCover doc comment). Must
+  // run before title derivation so extractFirstHeading scans the REST of
+  // the document, not any decorative markup inside the custom cover.
+  const { cover: customCoverHtml, rest: bodyAfterCover } = extractCustomCover(typographicHtml);
+
   // 4. Derive metadata (title from first H1 if not provided)
-  const derivedTitle = opts.title ?? extractFirstHeading(typographicHtml) ?? "Document";
+  const derivedTitle = opts.title ?? extractFirstHeading(bodyAfterCover) ?? "Document";
   const derivedAuthor = opts.author ?? "";
   const derivedDate = opts.date ?? formatToday();
 
@@ -113,22 +118,26 @@ export function render(opts: RenderOptions): RenderResult {
   const css = printCss(cssOptions);
 
   // 6. Assemble document
-  const coverBlock = opts.cover
-    ? buildCoverBlock({
-        title: derivedTitle,
-        subtitle: opts.subtitle,
-        author: derivedAuthor,
-        date: derivedDate,
-      })
-    : "";
+  // A custom cover (extracted above) takes priority over the built-in
+  // template — they're mutually exclusive, never combined.
+  const coverBlock = customCoverHtml
+    ? customCoverHtml
+    : opts.cover
+      ? buildCoverBlock({
+          title: derivedTitle,
+          subtitle: opts.subtitle,
+          author: derivedAuthor,
+          date: derivedDate,
+        })
+      : "";
 
   // TOC anchors must resolve: assign id="toc-N" to each H1-H3 in the same
   // order buildTocBlock scans them, or every TOC link is a dead href (masked
   // in PDFs by Chromium outline bookmarks, glaring in --to html). Headings
   // that already carry an id keep it — the ids array records the ACTUAL id
   // per heading so TOC entries always link to something real.
-  const anchored = opts.toc ? addHeadingIds(typographicHtml) : { html: typographicHtml, ids: [] };
-  const anchoredHtml = anchored.html;
+  const anchored = opts.toc ? addHeadingIds(bodyAfterCover) : { html: bodyAfterCover, ids: [] };
+  const anchoredHtml = wrapReferencesSection(anchored.html);
 
   const tocBlock = opts.toc
     ? buildTocBlock(anchoredHtml, anchored.ids)
@@ -368,6 +377,73 @@ function wrapChaptersByH1(html: string): string {
   return chunks.join("\n");
 }
 
+/**
+ * Wrap an APA-style "References" section in a `.references` container so
+ * print CSS can apply a hanging indent to each entry without touching
+ * ordinary body paragraphs. Detects an <h1> whose text is exactly
+ * "References" (case-insensitive) and wraps everything from there to the
+ * next <h1> (or end of document) in <div class="references">...</div>.
+ * The heading itself stays outside the wrapper so its own styling is
+ * unaffected. No-op if no such heading exists.
+ */
+function wrapReferencesSection(html: string): string {
+  const h1Re = /<h1\b[^>]*>([\s\S]*?)<\/h1>/gi;
+  let m: RegExpExecArray | null;
+  let headingStart = -1;
+  let headingEnd = -1;
+  while ((m = h1Re.exec(html)) !== null) {
+    const text = decodeTextEntities(stripTags(m[1])).trim().toLowerCase();
+    if (text === "references") {
+      headingStart = m.index;
+      headingEnd = m.index + m[0].length;
+      break;
+    }
+  }
+  if (headingStart === -1) return html;
+
+  // Find the next H1 after the References heading (end of section), or EOF.
+  const nextH1Re = /<h1\b[^>]*>/gi;
+  nextH1Re.lastIndex = headingEnd;
+  const next = nextH1Re.exec(html);
+  const sectionEnd = next ? next.index : html.length;
+
+  const before = html.slice(0, headingEnd);
+  const body = html.slice(headingEnd, sectionEnd);
+  const after = html.slice(sectionEnd);
+
+  return `${before}<div class="references">${body}</div>${after}`;
+}
+
+/**
+ * Extract a custom, fully-styled cover section from the very start of the
+ * document, so it can be slotted into the same position the built-in
+ * --cover template occupies (before the TOC), instead of being left as
+ * ordinary body content (which the assembly order in render() places
+ * AFTER the TOC — see the `coverBlock, tocBlock, chapterHtml` order below).
+ *
+ * Detects a top-level `<section class="ai4ld-cover" ...>...</section>`
+ * as the first non-whitespace content in the document. This is a distinct
+ * class from the tool's own generated `.cover` (buildCoverBlock) so the two
+ * mechanisms never collide — a document uses one or the other, never both.
+ * Callers should NOT also pass --cover when using a custom cover section.
+ *
+ * No nested-tag balancing: the custom cover section is expected to be a
+ * single flat block (divs/spans/hr, no inner <section>), so the first
+ * </section> after the opening tag is assumed to close it.
+ */
+function extractCustomCover(html: string): { cover: string; rest: string } {
+  const trimmed = html.replace(/^\s+/, "");
+  const openMatch = trimmed.match(/^<section\s+class="ai4ld-cover"[^>]*>/i);
+  if (!openMatch) return { cover: "", rest: html };
+  const closeIdx = trimmed.indexOf("</section>", openMatch[0].length);
+  if (closeIdx === -1) return { cover: "", rest: html };
+  const closeEnd = closeIdx + "</section>".length;
+  return {
+    cover: trimmed.slice(0, closeEnd),
+    rest: trimmed.slice(closeEnd),
+  };
+}
+
 function extractFirstHeading(html: string): string | null {
   const m = html.match(/<h1\b[^>]*>([\s\S]*?)<\/h1>/i);
   return m ? decodeTextEntities(stripTags(m[1]).trim()) : null;
diff --git a/make-pdf/src/smartypants.ts b/make-pdf/src/smartypants.ts
index 2dfe097e09..103d937837 100644
--- a/make-pdf/src/smartypants.ts
+++ b/make-pdf/src/smartypants.ts
@@ -20,7 +20,22 @@
 
 const CODE_ZONE_RE = /<(pre|code|script|style)\b[^>]*>[\s\S]*?<\/\1>/gi;
 const TAG_RE = /<[^>]+>/g;
-const URL_RE = /\bhttps?:\/\/\S+/g;
+// BUG FIX (2026-07-20): a bare autolinked URL like <a href="X">X</a> has
+// the URL text sitting with zero whitespace before its own closing </a>
+// tag. TAG_RE carves that </a> into a "\u0000SMARTPANTS_PRESERVED_N\u0000"
+// placeholder BEFORE this pattern runs. The old pattern (\S+, non-
+// whitespace-greedy) swallowed that adjacent placeholder into the URL
+// match, since \u0000 and the placeholder text are all non-whitespace.
+// The outer carve() then stored "https://...\u0000SMARTPANTS_PRESERVED_N\u0000"
+// as ONE preserved zone. String.replace() with a global regex does not
+// rescan replacement text for further matches, so that inner placeholder
+// was never restored -- it leaked through as literal "SMARTPANTS_PRESERVED_N"
+// text glued onto the end of the URL, corrupting the link (found in DOI
+// reference lists across the ebook PDFs). Excluding \u0000 from the URL
+// char class stops the match from ever crossing into an adjacent,
+// already-carved zone.
+const URL_RE = /\bhttps?:\/\/[^\s\u0000]+/g;
+
 
 /**
  * Apply smartypants to an HTML string. Zones that should not be touched:
diff --git a/make-pdf/test/render.test.ts b/make-pdf/test/render.test.ts
index b54085ecb2..8758b251f1 100644
--- a/make-pdf/test/render.test.ts
+++ b/make-pdf/test/render.test.ts
@@ -61,6 +61,30 @@ describe("smartypants", () => {
     expect(out).toContain(`href="it's-a-test.html"`);
   });
 
+  test("does NOT leak SMARTPANTS_PRESERVED placeholders into autolinked URLs", () => {
+    // Regression test: found 2026-07-20 in AI4LD ebook PDF reference
+    // lists. A bare autolinked URL (anchor text == href, zero whitespace
+    // before the closing tag) previously had its </a> placeholder
+    // swallowed by the URL regex's greedy \S+, leaking raw
+    // "SMARTPANTS_PRESERVED_N" text into the rendered link.
+    const input = `<p>See <a href="https://doi.org/10.1016/j.caeai.2026.100637">https://doi.org/10.1016/j.caeai.2026.100637</a> for details.</p>`;
+    const out = smartypants(input);
+    expect(out).not.toContain("SMARTPANTS_PRESERVED");
+    expect(out).toContain(
+      `<a href="https://doi.org/10.1016/j.caeai.2026.100637">https://doi.org/10.1016/j.caeai.2026.100637</a>`
+    );
+  });
+
+  test("does NOT leak placeholders when a linked URL is immediately followed by another tag", () => {
+    // Same bug, different adjacency: URL directly abutting a second tag
+    // (e.g. two consecutive auto-linked references with no separating
+    // whitespace) must not bleed a placeholder into either link.
+    const input = `<p><a href="https://a.example/x">https://a.example/x</a><a href="https://b.example/y">https://b.example/y</a></p>`;
+    const out = smartypants(input);
+    expect(out).not.toContain("SMARTPANTS_PRESERVED");
+    expect(out).toBe(input);
+  });
+
   test("does NOT convert -- in CLI flags", () => {
     // Prose like "try --verbose mode" should not turn -- into em dash
     const out = smartypants(`<p>Try --verbose mode.</p>`);
@@ -157,6 +181,72 @@ describe("render (end-to-end)", () => {
     expect(result.html).toContain("\u2014");
   });
 
+  test("wraps a References section for APA hanging-indent styling", () => {
+    const result = render({
+      markdown: `# My Ebook\n\nBody text.\n\n# References\n\nSmith, J. (2020). A paper.\n\nJones, K. (2021). Another paper.\n`,
+    });
+    expect(result.html).toMatch(
+      /<div class="references">[\s\S]*Smith, J\. \(2020\)[\s\S]*Jones, K\. \(2021\)[\s\S]*<\/div>/
+    );
+    // The heading itself stays outside the wrapper.
+    expect(result.html).not.toMatch(/<div class="references">\s*<h1/);
+  });
+
+  test("References wrapping is case-insensitive and a no-op with no such heading", () => {
+    const lower = render({ markdown: `# Doc\n\nBody.\n\n# references\n\nRef one.\n` });
+    expect(lower.html).toContain('<div class="references">');
+
+    const none = render({ markdown: `# Doc\n\nJust body text, no references section.\n` });
+    expect(none.html).not.toContain('<div class="references">');
+  });
+
+  test("extracts a custom .ai4ld-cover section and places it before the TOC", () => {
+    const result = render({
+      markdown: `<section class="ai4ld-cover" style="background:#05C7F2;">\n  <div>My Custom Cover</div>\n</section>\n\n# Real Title\n\nBody.\n`,
+      toc: true,
+    });
+    const coverIdx = result.html.indexOf("My Custom Cover");
+    const tocIdx = result.html.indexOf('<section class="toc">');
+    // "Body." (not "Real Title") — the TOC itself legitimately contains a
+    // link with the text "Real Title", which would make that string a false
+    // marker for body content; "Body." appears only in the real chapter.
+    const bodyIdx = result.html.indexOf("Body.");
+    expect(coverIdx).toBeGreaterThan(-1);
+    expect(tocIdx).toBeGreaterThan(-1);
+    expect(bodyIdx).toBeGreaterThan(-1);
+    // Custom cover must render BEFORE the TOC, which must render before body
+    // content — the bug this fixes: body content (including a cover
+    // written as ordinary markdown) always landed AFTER the TOC because
+    // the assembly order is coverBlock, tocBlock, chapterHtml, and only
+    // the built-in --cover template populated coverBlock.
+    expect(coverIdx).toBeLessThan(tocIdx);
+    expect(tocIdx).toBeLessThan(bodyIdx);
+  });
+
+  test("custom cover title text does not create a duplicate TOC entry", () => {
+    // The cover title must NOT be an <h1> (that's exactly what caused the
+    // duplicate-heading bug) — verify a same-titled <div> inside the
+    // custom cover isn't picked up as a second heading by the TOC.
+    const result = render({
+      markdown: `<section class="ai4ld-cover">\n  <div>Real Title</div>\n</section>\n\n# Real Title\n\nBody.\n`,
+      toc: true,
+    });
+    const matches = result.html.match(/<a[^>]*>Real Title<\/a>/g) ?? [];
+    expect(matches.length).toBe(1);
+  });
+
+  test("derives title from the real first H1, not text inside a custom cover", () => {
+    const result = render({
+      markdown: `<section class="ai4ld-cover">\n  <div>Not The Title</div>\n</section>\n\n# Actual Title\n\nBody.\n`,
+    });
+    expect(result.meta.title).toBe("Actual Title");
+  });
+
+  test("no custom cover present is a no-op (ordinary documents unaffected)", () => {
+    const result = render({ markdown: `# Just a doc\n\nNo cover here.\n` });
+    expect(result.html).not.toContain("ai4ld-cover");
+  });
+
   test("derives title from first H1 when --title is not passed", () => {
     const result = render({ markdown: `# My Title\n\nBody.` });
     expect(result.meta.title).toBe("My Title");
@@ -236,12 +326,19 @@ describe("render (end-to-end)", () => {
     expect(result.html).toContain("Safe");
   });
 
-  test("respects text-align: left — no justify in print CSS", () => {
+  test("respects text-align: left — no justify or first-line indent on body paragraphs", () => {
     const result = render({ markdown: `para1\n\npara2\n` });
-    // The rule from the design-review fix: no p + p indent, text-align: left.
+    // The rule from the design-review fix: no p + p first-line indent, text-align: left.
     expect(result.printCss).toContain("text-align: left");
     expect(result.printCss).not.toContain("text-align: justify");
-    expect(result.printCss).not.toContain("text-indent");
+    // Ordinary paragraphs (the bare `p { ... }` rule) must not carry a
+    // first-line text-indent. This does NOT ban text-indent everywhere —
+    // `.references p` intentionally uses a negative text-indent for the
+    // APA hanging-indent pattern (see the "wraps a References section"
+    // test above); scope the check to the base rule specifically.
+    const baseParagraphRule = result.printCss.match(/(?<!\.references )\bp\s*\{[^}]*\}/);
+    expect(baseParagraphRule?.[0]).toBeDefined();
+    expect(baseParagraphRule?.[0]).not.toContain("text-indent");
   });
 
   test("includes CJK font fallback in body", () => {