quarto-dev · cscheid · Feb 20, 2026 · Feb 19, 2026 · Feb 19, 2026 · Feb 19, 2026
diff --git a/src/project/types/website/website-llms.ts b/src/project/types/website/website-llms.ts
@@ -8,7 +8,7 @@ import { basename, join, relative } from "../../../deno_ral/path.ts";
 import { existsSync } from "../../../deno_ral/fs.ts";
 import { pathWithForwardSlashes } from "../../../core/path.ts";
 
-import { Document, Element } from "../../../core/deno-dom.ts";
+import { Document, Element, Node } from "../../../core/deno-dom.ts";
 import { execProcess } from "../../../core/process.ts";
 import { pandocBinaryPath, resourcePath } from "../../../core/resources.ts";
 
@@ -83,9 +83,36 @@ export function llmsHtmlFinalizer(
 
     // Convert HTML to markdown using Pandoc with the llms.lua filter
     await convertHtmlToLlmsMarkdown(htmlContent, llmsOutputPath);
+
+    // Clean up conditional content markers from the original HTML doc
+    cleanupConditionalContent(doc);
   };
 }
 
+/**
+ * Clean up conditional content markers from the HTML document.
+ * - Remove llms-only content (should not appear in HTML output)
+ * - Unwrap llms-hidden markers (keep content, remove wrapper div)
+ */
+function cleanupConditionalContent(doc: Document): void {
+  // Remove llms-only content from HTML output
+  for (const el of doc.querySelectorAll(".llms-conditional-content")) {
+    (el as Element).remove();
+  }
+
+  // Unwrap llms-hidden markers (keep content, remove wrapper div)
+  for (const el of doc.querySelectorAll(".llms-hidden-content")) {
+    const parent = (el as Element).parentElement;
+    if (parent) {
+      const element = el as Element;
+      while (element.firstChild) {
+        parent.insertBefore(element.firstChild as Node, element as Node);
+      }
+      element.remove();
+    }
+  }
+}
+
 /**
  * Extract the main content from an HTML document, removing navigation,
  * sidebars, footers, scripts, and styles.
@@ -104,6 +131,7 @@ function extractMainContent(doc: Document): string {
     ".sidebar",
     ".quarto-search",
     "nav.navbar",
+    ".quarto-page-breadcrumbs",
     "script",
     "style",
     "link[rel='stylesheet']",
@@ -128,6 +156,9 @@ function extractMainContent(doc: Document): string {
     return "";
   }
 
+  // Preprocess annotated code blocks before converting to markdown
+  preprocessAnnotatedCodeBlocks(clone, main as Element);
+
   // Return a minimal HTML document with just the content
   return `<!DOCTYPE html>
 <html>
@@ -138,6 +169,65 @@ ${main.innerHTML}
 </html>`;
 }
 
+/**
+ * Preprocess annotated code blocks for llms output.
+ * Restores original code text (with annotation markers) and converts
+ * the annotation definition list to an ordered list.
+ */
+function preprocessAnnotatedCodeBlocks(doc: Document, container: Element): void {
+  // Restore original code text in annotated code blocks.
+  // The llms-code-annotations.lua filter saves the original text
+  // (before code-annotation.lua strips markers) as a data attribute.
+  const annotated = container.querySelectorAll("[data-llms-code-original]");
+  for (const node of annotated) {
+    const el = node as Element;
+    const originalText = el.getAttribute("data-llms-code-original");
+    if (!originalText) continue;
+
+    // The attribute is on the wrapper div; find the <code> element inside
+    const codeEl = el.tagName === "CODE"
+      ? el
+      : el.querySelector("code") as Element | null;
+    if (codeEl) {
+      // Replace content with original (removes syntax highlighting spans + annotation buttons)
+      codeEl.textContent = originalText;
+    }
+
+    el.removeAttribute("data-llms-code-original");
+  }
+
+  // Remove annotation gutter elements
+  const gutters = container.querySelectorAll(
+    ".code-annotation-gutter, .code-annotation-gutter-bg",
+  );
+  for (const gutter of gutters) {
+    (gutter as Element).remove();
+  }
+
+  // Convert annotation definition lists to ordered lists.
+  // The annotation text is in <dd> elements; <dt> elements have just the number.
+  const dls = container.querySelectorAll("dl.code-annotation-container-grid");
+  for (const dlNode of dls) {
+    const dl = dlNode as Element;
+    const ol = doc.createElement("ol");
+    const dds = dl.querySelectorAll("dd");
+    for (const ddNode of dds) {
+      const dd = ddNode as Element;
+      const li = doc.createElement("li");
+      li.innerHTML = dd.innerHTML;
+      ol.appendChild(li);
+    }
+
+    // Replace the DL (and its cell-annotation wrapper div if present)
+    const parent = dl.parentElement;
+    if (parent && parent.classList.contains("cell-annotation")) {
+      parent.parentElement?.replaceChild(ol, parent);
+    } else {
+      dl.parentElement?.replaceChild(ol, dl);
+    }
+  }
+}
+
 /**
  * Convert HTML content to markdown using Pandoc with the llms.lua filter.
  */

diff --git a/src/project/types/website/website.ts b/src/project/types/website/website.ts
@@ -32,6 +32,7 @@ import { projectOffset, projectOutputDir } from "../../project-shared.ts";
 import { isHtmlFileOutput } from "../../../config/format.ts";
 
 import {
+  kFilterParams,
   kIncludeInHeader,
   kPageTitle,
   kTitle,
@@ -358,6 +359,8 @@ export const websiteProjectType: ProjectType = {
 
     // Add llms.txt finalizer if enabled
     if (websiteConfigBoolean(kLlmsTxt, false, project.config)) {
+      extras[kFilterParams] = extras[kFilterParams] || {};
+      extras[kFilterParams]["llms-txt"] = true;
       extras.html[kHtmlFinalizers]?.push(
         llmsHtmlFinalizer(source, project, format),
       );

diff --git a/src/resources/filters/llms/llms.lua b/src/resources/filters/llms/llms.lua
@@ -15,6 +15,7 @@ local skippable_classes = {
     ["quarto-float"] = true,
     ["quarto-float-fig"] = true,
     ["figure"] = true,
+    ["llms-conditional-content"] = true,
 }
 local droppable_classes = {
     ["navbar-container"] = true,
@@ -25,6 +26,8 @@ local droppable_classes = {
     ["listing-categories"] = true,
     ["quarto-listing-category"] = true,  -- category filter sidebar
     ["listing-category"] = true,  -- individual category badges
+    ["quarto-page-breadcrumbs"] = true,  -- breadcrumb navigation
+    ["llms-hidden-content"] = true,
 }
 local droppable_ids = {
     ["quarto-header"] = true,
@@ -70,6 +73,53 @@ local function clean_element(el)
     end
 end
 
+local function handle_tabset(div)
+    local titles = {}
+    local panes = {}
+
+    -- Extract tab titles from the nav BulletList (first one in the div)
+    -- and tab pane contents from the tab-content Div
+    for _, block in ipairs(div.content) do
+        if block.t == "BulletList" and #titles == 0 then
+            for _, item in ipairs(block.content) do
+                for _, inner_block in ipairs(item) do
+                    if inner_block.t == "Plain" or inner_block.t == "Para" then
+                        for _, inline in ipairs(inner_block.content) do
+                            if inline.t == "Link" then
+                                table.insert(titles, inline.content)
+                                break
+                            end
+                        end
+                    end
+                end
+            end
+        elseif block.t == "Div" and block.classes:includes("tab-content") then
+            for _, inner in ipairs(block.content) do
+                if inner.t == "Div" and inner.classes:includes("tab-pane") then
+                    table.insert(panes, inner.content)
+                end
+            end
+        end
+    end
+
+    -- Build output: heading + content for each tab
+    local result = pandoc.Blocks({})
+    for i = 1, math.max(#titles, #panes) do
+        if titles[i] then
+            result:insert(pandoc.Header(2, titles[i]))
+        end
+        if panes[i] then
+            result:extend(panes[i])
+        end
+    end
+
+    if #result > 0 then
+        return result
+    end
+    -- Fallback: return content as-is
+    return div.content
+end
+
 local function handle_callout(div)
     local kind = "NOTE" -- NOTE, TIP, IMPORTANT, WARNING, CAUTION
     div.classes:map(function(cls)
@@ -140,8 +190,10 @@ function Link(link)
         return link.content
     end
 
-    if link.target and link.target:match("%.html$") then
+    if link.target and (link.target:match("%.html$") or link.target:match("%.html#")) then
+        link.target = link.target:gsub("%.html#", ".llms.md#")
         link.target = link.target:gsub("%.html$", ".llms.md")
+        link.target = link.target:gsub("^%./", "")
         if link.classes:includes("btn") then
             link.attr = pandoc.Attr()
         end
@@ -174,6 +226,10 @@ end
 
 function Div(div)
 
+    if div.classes:includes("panel-tabset") then
+        return handle_tabset(div)
+    end
+
     if div.classes:includes("callout") then
         return handle_callout(div)
     end

diff --git a/src/resources/filters/main.lua b/src/resources/filters/main.lua
@@ -143,6 +143,8 @@ import("./quarto-pre/bibliography-formats.lua")
 import("./quarto-pre/book-links.lua")
 import("./quarto-pre/book-numbering.lua")
 import("./quarto-pre/code-annotation.lua")
+import("./quarto-pre/llms-code-annotations.lua")
+import("./quarto-pre/llms-conditional-content.lua")
 import("./quarto-pre/code-filename.lua")
 import("./quarto-pre/contentsshortcode.lua")
 import("./quarto-pre/engine-escape.lua")
@@ -321,6 +323,15 @@ local quarto_pre_filters = {
     traverser = 'jog',
   },
 
+  { name = "pre-llms-conditional-content",
+    filter = filterIf(
+      function() return param("llms-txt", false) end,
+      llms_resolve_conditional_content()
+    ),
+    flags = { "has_conditional_content" },
+    traverser = 'jog',
+  },
+
   { name = "pre-combined-hidden",
     filter = combineFilters({
       hidden(),
@@ -336,6 +347,15 @@ local quarto_pre_filters = {
     traverser = 'jog',
   },
 
+  { name = "pre-llms-save-code-annotations",
+    filter = filterIf(
+      function() return param("llms-txt", false) end,
+      llms_save_code_annotations()
+    ),
+    flags = { "has_code_annotations" },
+    traverser = 'jog',
+  },
+
   { name = "pre-code-annotations",
     filter = code_annotations(),
     flags = { "has_code_annotations" },

diff --git a/src/resources/filters/quarto-pre/llms-code-annotations.lua b/src/resources/filters/quarto-pre/llms-code-annotations.lua
@@ -0,0 +1,16 @@
+-- llms-code-annotations.lua
+-- Copyright (C) 2020-2026 Posit Software, PBC
+--
+-- Saves original CodeBlock text before code-annotation.lua strips markers.
+-- Only runs when llms-txt is enabled (guarded by filterIf in main.lua).
+
+function llms_save_code_annotations()
+  return {
+    CodeBlock = function(el)
+      if el.text:match("<%d+>") then
+        el.attributes["data-llms-code-original"] = el.text
+      end
+      return el
+    end
+  }
+end
diff --git a/src/resources/filters/quarto-pre/llms-conditional-content.lua b/src/resources/filters/quarto-pre/llms-conditional-content.lua
@@ -0,0 +1,56 @@
+-- llms-conditional-content.lua
+-- Copyright (C) 2020-2026 Posit Software, PBC
+--
+-- Pre-filter that intercepts ConditionalBlock nodes referencing llms-txt
+-- and replaces them with marker Divs so content can be included/excluded
+-- from llms.md output independently of the HTML format.
+-- Only runs when llms-txt is enabled (guarded by filterIf in main.lua).
+
+function llms_resolve_conditional_content()
+  -- Determine if a ConditionalBlock should be visible for llms-txt output.
+  -- Returns true (include), false (exclude), or nil (no llms-txt condition).
+  local function is_llms_visible(tbl)
+    local constants = require("modules/constants")
+    local function list_contains(list, value)
+      if not list then return false end
+      for _, v in ipairs(list) do
+        if v == value then return true end
+      end
+      return false
+    end
+
+    local cond = tbl.condition
+    local has_when = list_contains(cond[constants.kWhenFormat], "llms-txt")
+    local has_unless = list_contains(cond[constants.kUnlessFormat], "llms-txt")
+
+    if not has_when and not has_unless then return nil end
+
+    if tbl.behavior == constants.kContentVisible then
+      -- content-visible when-format="llms-txt" -> include for llms
+      -- content-visible unless-format="llms-txt" -> exclude for llms
+      return has_when
+    else -- content-hidden
+      -- content-hidden when-format="llms-txt" -> exclude for llms
+      -- content-hidden unless-format="llms-txt" -> include for llms
+      return has_unless
+    end
+  end
+
+  return {
+    ConditionalBlock = function(tbl)
+      local llms_visible = is_llms_visible(tbl)
+      if llms_visible == nil then return nil end
+
+      local html_visible = is_visible(tbl)  -- from content-hidden.lua
+      if llms_visible == html_visible then return nil end  -- no intervention needed
+
+      local div = tbl.original_node:clone()
+      if llms_visible then
+        div.classes:insert("llms-conditional-content")
+      else
+        div.classes:insert("llms-hidden-content")
+      end
+      return div
+    end
+  }
+end
diff --git a/tests/docs/smoke-all/website/llms-txt/_quarto.yml b/tests/docs/smoke-all/website/llms-txt/_quarto.yml
@@ -11,6 +11,11 @@ website:
       - href: index.qmd
         text: Home
       - about.qmd
+  sidebar:
+    contents:
+      - section: Info
+        contents:
+          - about.qmd
 
 format:
   html: