diff --git a/configuration b/configuration
index 63c8647e469..fa8bac417cb 100644
--- a/configuration
+++ b/configuration
@@ -14,10 +14,10 @@
 export DENO=v2.4.5
 # TODO figure out where 0.1.41 apple silicon libs are available
 export DENO_DOM=v0.1.41-alpha-artifacts
-export PANDOC=3.6.3
+export PANDOC=3.8.3
 export DARTSASS=1.87.0
 export ESBUILD=0.25.10
-export TYPST=0.13.0
+export TYPST=0.14.2
 
 
 # NB: we can't put comments in the same line as export statements because it
diff --git a/dev-docs/update-pandoc-checklist.md b/dev-docs/update-pandoc-checklist.md
index ac3115da0ad..e59a80321d1 100644
--- a/dev-docs/update-pandoc-checklist.md
+++ b/dev-docs/update-pandoc-checklist.md
@@ -2,10 +2,30 @@
 
 Carlos needs to run this:
 
-- [ ] Ensure archives are upgraded
-- [ ] Run `AWS_PROFILE=... ./package/src/quarto-bld update-pandoc PANDOC_VERSION`
+- [x] Ensure archives are upgraded
+- [x] Run `AWS_PROFILE=... ./package/src/quarto-bld update-pandoc PANDOC_VERSION`
 - [ ] look at `git diff`, specifically for changes in Pandoc templates, and adjust as needed.
 
+As a reminder, our templates are kept in the same directories as Pandoc's templates, but with different names. `git diff` will show the diff in Pandoc's template; we have to manually patch
+ours. (We can't just use `patch` because the templates have diverged too much)
+
+### Pandoc templates
+
+The general rule for the naming is that "format.template" indicates Pandoc naming, and "template.format" indicates ours. Examples below:
+
+#### beamer
+
+- Pandoc's: src/resources/formats/beamer/pandoc/beamer.template
+- Ours: src/resources/formats/beamer/pandoc/template.tex
+
+Partials:
+
+- Pandoc's:
+  - src/resources/formats/beamer/pandoc/latex.common
+- Ours:
+  - src/resources/formats/beamer/pandoc/common.latex
+
+
 ## Manual steps
 
 - [ ] Update schemas by inspecting [their changelog](https://github.com/jgm/pandoc/blob/main/changelog.md) for new commands, deprecation removals, etc
diff --git a/llm-docs/pandoc-quarto-typst-templates.md b/llm-docs/pandoc-quarto-typst-templates.md
new file mode 100644
index 00000000000..7739ea44f3c
--- /dev/null
+++ b/llm-docs/pandoc-quarto-typst-templates.md
@@ -0,0 +1,210 @@
+# Pandoc and Quarto Typst Templates
+
+This document describes how Quarto integrates Pandoc's typst templates and transforms them into a more modular structure suitable for Quarto's extended functionality.
+
+## 1. How Pandoc Templates Are Copied into Quarto
+
+The `writePandocTemplates` function in `package/src/common/update-pandoc.ts` handles copying Pandoc's templates into Quarto's resources during the Pandoc update process.
+
+### Source and Destination
+
+- **Source**: Pandoc templates are downloaded from the Pandoc GitHub repository's `data/templates/` directory
+- **Destination**: `src/resources/formats/typst/pandoc/`
+
+### Files Copied
+
+Two files are copied from Pandoc for typst support:
+
+| Pandoc Source | Quarto Destination |
+|---------------|-------------------|
+| `default.typst` | `typst.template` |
+| `template.typst` | `template.typst` (unchanged name) |
+
+### Purpose of Each Pandoc File
+
+**default.typst** (becomes `typst.template`): The main Pandoc template that orchestrates the document structure. It:
+- Defines a horizontal rule helper
+- Sets up term list rendering with indented descriptions
+- Configures table styling with no strokes
+- Sets figure caption positions for tables (top) and images (bottom)
+- Optionally includes syntax highlighting definitions
+- Either imports a user-provided template or inlines the `template.typst` content via `$template.typst()$`
+- Disables smart quotes if not enabled
+- Processes header-includes
+- Invokes the `conf()` function with all document metadata
+- Renders include-before content, TOC, body, bibliography, and include-after content
+
+**template.typst**: Defines the `conf()` document function and helpers. It:
+- Provides a `content-to-string` helper to extract text from content nodes
+- Defines `conf()` which accepts all document metadata parameters
+- Sets document metadata (title, keywords, author) for PDF accessibility
+- Configures page, paragraph, text, and heading settings
+- Applies link, reference, and file colors
+- Renders the title block with optional thanks footnote
+- Returns the document content
+
+## 2. Quarto's Modular Template Structure
+
+Quarto breaks the Pandoc templates into a modular structure in `src/resources/formats/typst/pandoc/quarto/`. This allows for:
+- Better separation of concerns
+- Easier customization and extension
+- Support for Quarto-specific features (brand typography, callouts, subfloats)
+
+### Template Files
+
+The `typstFormat` function in `src/format/typst/format-typst.ts` configures the template context, specifying `template.typ` as the main template with these partials: `definitions.typ`, `typst-template.typ`, `page.typ`, `typst-show.typ`, `notes.typ`, and `biblio.typ`.
+
+### template.typ - The Orchestrator
+
+Assembles the document by including all partials in order:
+1. `definitions.typ()` - utility definitions
+2. `typst-template.typ()` - the article function
+3. Header-includes loop
+4. `page.typ()` - page configuration
+5. `typst-show.typ()` - applies the article function
+6. Include-before loop
+7. Body
+8. `notes.typ()` - endnotes handling
+9. `biblio.typ()` - bibliography
+10. Include-after loop
+
+### definitions.typ - Utility Definitions
+
+Combines Pandoc definitions with Quarto-specific functionality:
+
+**From Pandoc**:
+- `content-to-string` helper to extract text from content nodes (used for PDF metadata and link colors)
+- `horizontalrule` definition for horizontal rules
+- Term list show rule with indented descriptions
+- Code highlighting definitions (conditionally included)
+
+**Quarto additions**:
+- `endnote` helper for endnote rendering
+- Code block styling (gray background, padding, rounded corners)
+- `block_with_new_content` helper for reconstructing blocks with modified content
+- `empty` function to check if content is empty (handles strings and content nodes)
+- Subfloat support via `quartosubfloatcounter` and `quarto_super` function for nested figures with sub-numbering
+- Callout figure show rule that transforms callout figures with proper titles and cross-reference numbering
+- `callout` function for rendering callout boxes with customizable colors, icons, and styling
+
+### typst-template.typ - The Article Function
+
+Corresponds to `conf()` in Pandoc's `template.typst`. Defines the `article()` function with these parameters:
+
+**Document Metadata** (from Pandoc):
+- `title`, `subtitle`, `authors`, `keywords`, `date`
+- `abstract-title`, `abstract`, `thanks`
+
+**Layout** (from Pandoc):
+- `cols`, `lang`, `region`
+
+**Typography** (from Pandoc):
+- `font`, `fontsize`, `mathfont`, `codefont`, `linestretch`, `sectionnumbering`
+- `linkcolor`, `citecolor`, `filecolor`
+
+**Quarto Extensions**:
+- `title-size`, `subtitle-size` for customizable title sizing
+- `heading-family`, `heading-weight`, `heading-style`, `heading-color`, `heading-line-height` for brand typography
+- `toc`, `toc_title`, `toc_depth`, `toc_indent` for integrated table of contents
+
+**Functionality**:
+- Sets `document()` metadata (title, keywords, author string) for PDF accessibility
+- Configures paragraph justification and leading from `linestretch`
+- Applies conditional font settings using `set ... if` pattern (Typst 0.14+)
+- Applies link colors using `content-to-string` helper
+- Renders the title block with thanks footnote, author grid, date, and abstract
+- Optionally renders table of contents
+- Handles single or multi-column layout
+
+### page.typ - Page Configuration
+
+Extracted from Pandoc's `conf()` function to allow independent page setup:
+- Sets paper size (defaults to "us-letter")
+- Sets margins (defaults to x: 1.25in, y: 1.25in)
+- Sets page numbering
+- Sets column count
+- Optionally sets a background logo image with configurable location, inset, width, and alt text (Quarto extension)
+
+### typst-show.typ - Parameter Mapping
+
+Applies the `article()` function via a show rule, mapping Pandoc metadata and brand.yaml values to parameters. Follows precedence rules where Pandoc metadata takes priority and brand.yaml provides fallbacks.
+
+**Pandoc Metadata Mappings**:
+- `title`, `subtitle`, `date`, `abstract` → direct pass-through
+- `by-author` → `authors` (uses Quarto's author normalization with `it.name.literal` and `it.affiliations`)
+- `labels.abstract` → `abstract-title` (localized)
+- `mainfont` → `font`
+- `fontsize` → `fontsize`
+- `mathfont` → `mathfont`
+- `codefont` → `codefont`
+- `linestretch` → `linestretch`
+- `section-numbering` → `sectionnumbering`
+- `thanks` → `thanks`
+- `linkcolor`, `citecolor`, `filecolor` → link color parameters
+- `keywords` → `keywords`
+- `toc`, `toc-title`, `toc-depth`, `toc-indent` → TOC parameters
+- `columns` → `cols`
+
+**Brand.yaml Fallbacks** (used when Pandoc metadata not set):
+- `brand.typography.base.family` → `font`
+- `brand.typography.base.size` → `fontsize`
+- `brand.typography.monospace.family` → `codefont`
+- `brand.typography.headings.family` → `heading-family`
+- `brand.typography.headings.weight` → `heading-weight`
+- `brand.typography.headings.style` → `heading-style`
+- `brand.typography.headings.color` → `heading-color`
+- `brand.typography.headings.line-height` → `heading-line-height`
+
+### notes.typ - Endnotes Section
+
+Renders endnotes when present:
+- Adds vertical space and a horizontal rule
+- Sets smaller text size (0.88em)
+- Renders the notes content
+
+### biblio.typ - Bibliography
+
+Handles bibliography rendering:
+- Sets bibliography style from CSL file or bibliography style option
+- Renders bibliography from specified files
+
+### typst.template - Reference Copy
+
+This is the copy of Pandoc's `default.typst`, kept for reference. It is used when rendering without Quarto's template context (e.g., when a user provides a custom template).
+
+## 3. Parameter Summary Table
+
+| Pandoc Parameter | Quarto Parameter | Brand.yaml Fallback | Notes |
+|-----------------|------------------|---------------------|-------|
+| `title` | `title` | - | |
+| `subtitle` | `subtitle` | - | |
+| `author` | `authors` | - | Normalized via `by-author` |
+| `keywords` | `keywords` | - | Array of quoted strings |
+| `date` | `date` | - | |
+| `abstract` | `abstract` | - | |
+| `abstract-title` | `abstract-title` | `labels.abstract` | Localized |
+| `thanks` | `thanks` | - | Title footnote |
+| `mainfont` | `font` | `brand.typography.base.family` | |
+| `fontsize` | `fontsize` | `brand.typography.base.size` | |
+| `mathfont` | `mathfont` | - | |
+| `codefont` | `codefont` | `brand.typography.monospace.family` | |
+| `linestretch` | `linestretch` | - | Multiplied by 0.65em for leading |
+| `section-numbering` | `sectionnumbering` | - | |
+| `linkcolor` | `linkcolor` | - | Hex color string |
+| `citecolor` | `citecolor` | - | Hex color string |
+| `filecolor` | `filecolor` | - | Hex color string |
+| `columns` | `cols` | - | |
+| `papersize` | (in page.typ) | - | |
+| `margin` | (in page.typ) | - | |
+| `page-numbering` | (in page.typ) | - | |
+| - | `title-size` | - | Quarto extension |
+| - | `subtitle-size` | - | Quarto extension |
+| - | `heading-family` | `brand.typography.headings.family` | Quarto extension |
+| - | `heading-weight` | `brand.typography.headings.weight` | Quarto extension |
+| - | `heading-style` | `brand.typography.headings.style` | Quarto extension |
+| - | `heading-color` | `brand.typography.headings.color` | Quarto extension |
+| - | `heading-line-height` | `brand.typography.headings.line-height` | Quarto extension |
+| `toc` | `toc` | - | |
+| `toc-title` | `toc_title` | - | |
+| `toc-depth` | `toc_depth` | - | |
+| `toc-indent` | `toc_indent` | - | Quarto extension |
diff --git a/src/command/check/check.ts b/src/command/check/check.ts
index 97c349dc820..c74afe9592d 100644
--- a/src/command/check/check.ts
+++ b/src/command/check/check.ts
@@ -245,16 +245,16 @@ async function checkVersions(conf: CheckConfiguration) {
   // with our installers
   const checkData: [string | undefined, string, string][] = strict
     ? [
-      [pandocVersion, "3.6.3", "Pandoc"],
+      [pandocVersion, "3.8.3", "Pandoc"],
       [sassVersion, "1.87.0", "Dart Sass"],
       [denoVersion, "2.4.5", "Deno"],
-      [typstVersion, "0.13.0", "Typst"],
+      [typstVersion, "0.14.0", "Typst"],
     ]
     : [
-      [pandocVersion, ">=3.6.3", "Pandoc"],
+      [pandocVersion, ">=3.8.3", "Pandoc"],
       [sassVersion, ">=1.87.0", "Dart Sass"],
       [denoVersion, ">=2.3.1", "Deno"],
-      [typstVersion, ">=0.13.0", "Typst"],
+      [typstVersion, ">=0.14.0", "Typst"],
     ];
   const fun = strict ? strictCheckVersion : checkVersion;
   for (const [version, constraint, name] of checkData) {
diff --git a/src/execute/engine-shared.ts b/src/execute/engine-shared.ts
deleted file mode 100644
index e0b9e14a52d..00000000000
--- a/src/execute/engine-shared.ts
+++ /dev/null
@@ -1,49 +0,0 @@
-/*
- * engine-shared.ts
- *
- * Copyright (C) 2021-2022 Posit Software, PBC
- */
-
-import { dirname, isAbsolute, join } from "../deno_ral/path.ts";
-
-import { restorePreservedHtml } from "../core/jupyter/preserve.ts";
-import { PostProcessOptions } from "./types.ts";
-
-export function postProcessRestorePreservedHtml(options: PostProcessOptions) {
-  // read the output file
-
-  const outputPath = isAbsolute(options.output)
-    ? options.output
-    : join(dirname(options.target.input), options.output);
-  let output = Deno.readTextFileSync(outputPath);
-
-  // substitute
-  output = restorePreservedHtml(
-    output,
-    options.preserve,
-  );
-
-  // re-write the output
-  Deno.writeTextFileSync(outputPath, output);
-}
-
-export function languagesInMarkdownFile(file: string) {
-  return languagesInMarkdown(Deno.readTextFileSync(file));
-}
-
-export function languagesInMarkdown(markdown: string) {
-  // see if there are any code chunks in the file
-  const languages = new Set<string>();
-  const kChunkRegex = /^[\t >]*```+\s*\{([a-zA-Z0-9_]+)( *[ ,].*)?\}\s*$/gm;
-  kChunkRegex.lastIndex = 0;
-  let match = kChunkRegex.exec(markdown);
-  while (match) {
-    const language = match[1].toLowerCase();
-    if (!languages.has(language)) {
-      languages.add(language);
-    }
-    match = kChunkRegex.exec(markdown);
-  }
-  kChunkRegex.lastIndex = 0;
-  return languages;
-}
diff --git a/src/execute/engine.ts b/src/execute/engine.ts
index 497b8262aa0..44b4b1fa7b6 100644
--- a/src/execute/engine.ts
+++ b/src/execute/engine.ts
@@ -27,7 +27,7 @@ import {
   ExecutionTarget,
   kQmdExtensions,
 } from "./types.ts";
-import { languagesInMarkdown } from "./engine-shared.ts";
+import { languagesInMarkdown } from "../core/pandoc/pandoc-partition.ts";
 import { languages as handlerLanguages } from "../core/handlers/base.ts";
 import { RenderContext, RenderFlags } from "../command/render/types.ts";
 import { mergeConfigs } from "../core/config.ts";
diff --git a/src/execute/ojs/compile.ts b/src/execute/ojs/compile.ts
index cc33bc02b39..e87cbeb6dde 100644
--- a/src/execute/ojs/compile.ts
+++ b/src/execute/ojs/compile.ts
@@ -65,7 +65,7 @@ import { logError } from "../../core/log.ts";
 import { breakQuartoMd, QuartoMdCell } from "../../core/lib/break-quarto-md.ts";
 
 import { MappedString } from "../../core/mapped-text.ts";
-import { languagesInMarkdown } from "../engine-shared.ts";
+import { languagesInMarkdown } from "../../core/pandoc/pandoc-partition.ts";
 
 import {
   pandocBlock,
diff --git a/src/resources/filters/quarto-post/typst-brand-yaml.lua b/src/resources/filters/quarto-post/typst-brand-yaml.lua
index 3ca5be17bb7..f23190d727c 100644
--- a/src/resources/filters/quarto-post/typst-brand-yaml.lua
+++ b/src/resources/filters/quarto-post/typst-brand-yaml.lua
@@ -170,11 +170,12 @@ function render_typst_brand_yaml()
           end
         end
 
+        -- monospace font family is handled by codefont in typst-template.typ via typst-show.typ
+        -- here we only handle properties that Pandoc doesn't support: weight, size, color
         local monospaceInline = _quarto.modules.brand.get_typography(brandMode, 'monospace-inline')
         if monospaceInline and next(monospaceInline) then
             quarto.doc.include_text('in-header', table.concat({
               '#show raw.where(block: false): set text(',
-              conditional_entry('font', monospaceInline.family and _quarto.modules.typst.css.translate_font_family_list(monospaceInline.family), false),
               conditional_entry('weight', _quarto.modules.typst.css.translate_font_weight(monospaceInline.weight)),
               conditional_entry('size', monospaceInline.size, false),
               conditional_entry('fill', monospaceInline.color, false),
@@ -189,11 +190,12 @@ function render_typst_brand_yaml()
           }))
         end
     
+        -- monospace font family is handled by codefont in typst-template.typ via typst-show.typ
+        -- here we only handle properties that Pandoc doesn't support: weight, size, color
         local monospaceBlock = _quarto.modules.brand.get_typography(brandMode, 'monospace-block')
         if monospaceBlock and next(monospaceBlock) then
           quarto.doc.include_text('in-header', table.concat({
             '#show raw.where(block: true): set text(',
-            conditional_entry('font', monospaceBlock.family and _quarto.modules.typst.css.translate_font_family_list(monospaceBlock.family), false),
             conditional_entry('weight', _quarto.modules.typst.css.translate_font_weight(monospaceBlock.weight)),
             conditional_entry('size', monospaceBlock.size, false),
             conditional_entry('fill', monospaceBlock.color, false),
@@ -307,7 +309,7 @@ function render_typst_brand_yaml()
           inset = '0.75in'
         end
         logoOptions.width = _quarto.modules.typst.css.translate_length(logoOptions.width or '1.5in')
-        logoOptions.inset = inset
+        logoOptions.inset = pandoc.RawInline('typst', inset)
         logoOptions.location = logoOptions.location and
           location_to_typst_align(logoOptions.location) or 'left+top'
         quarto.log.debug('logo options', logoOptions)
@@ -356,6 +358,13 @@ function render_typst_brand_yaml()
           ['line-height'] = line_height_to_leading(headings['line-height'] or base['line-height']),
         }
       end
+
+      local monospace = _quarto.modules.brand.get_typography(brandMode, 'monospace')
+      if monospace and monospace.family then
+        meta.brand.typography.monospace = {
+          family = pandoc.RawInline('typst', _quarto.modules.typst.css.translate_font_family_list(monospace.family)),
+        }
+      end
       return meta
     end,
   }
diff --git a/src/resources/formats/beamer/pandoc/babel-lang.tex b/src/resources/formats/beamer/pandoc/babel-lang.tex
index f29c833cb1e..ad1cc90c499 100644
--- a/src/resources/formats/beamer/pandoc/babel-lang.tex
+++ b/src/resources/formats/beamer/pandoc/babel-lang.tex
@@ -3,9 +3,9 @@
 $--
 $if(lang)$
 \ifLuaTeX
-\usepackage[bidi=basic$for(babeloptions)$,$babeloptions$$endfor$]{babel}
+\usepackage[bidi=basic,shorthands=off,$for(babeloptions)$,$babeloptions$$endfor$]{babel}
 \else
-\usepackage[bidi=default$for(babeloptions)$,$babeloptions$$endfor$]{babel}
+\usepackage[bidi=default,shorthands=off,$for(babeloptions)$,$babeloptions$$endfor$]{babel}
 \fi
 $if(babel-lang)$
 $if(mainfont)$
@@ -18,12 +18,7 @@
 $for(babelfonts/pairs)$
 \babelfont[$babelfonts.key$]{rm}{$babelfonts.value$}
 $endfor$
-% get rid of language-specific shorthands (see #6817):
-\let\LanguageShortHands\languageshorthands
-\def\languageshorthands#1{}
-$if(selnolig-langs)$
 \ifLuaTeX
-  \usepackage[$for(selnolig-langs)$$it$$sep$,$endfor$]{selnolig} % disable illegal ligatures
+  \usepackage{selnolig} % disable illegal ligatures
 \fi
-$endif$
 $endif$
\ No newline at end of file
diff --git a/src/resources/formats/beamer/pandoc/latex.common b/src/resources/formats/beamer/pandoc/latex.common
index 3f93b1b883a..cb745941de6 100644
--- a/src/resources/formats/beamer/pandoc/latex.common
+++ b/src/resources/formats/beamer/pandoc/latex.common
@@ -183,9 +183,9 @@ $-- Babel language support
 $--
 $if(lang)$
 \ifLuaTeX
-\usepackage[bidi=basic$for(babeloptions)$,$babeloptions$$endfor$]{babel}
+\usepackage[bidi=basic,shorthands=off,$for(babeloptions)$,$babeloptions$$endfor$]{babel}
 \else
-\usepackage[bidi=default$for(babeloptions)$,$babeloptions$$endfor$]{babel}
+\usepackage[bidi=default,shorthands=off,$for(babeloptions)$,$babeloptions$$endfor$]{babel}
 \fi
 $if(babel-lang)$
 $if(mainfont)$
@@ -198,15 +198,10 @@ $endif$
 $for(babelfonts/pairs)$
 \babelfont[$babelfonts.key$]{rm}{$babelfonts.value$}
 $endfor$
-% get rid of language-specific shorthands (see #6817):
-\let\LanguageShortHands\languageshorthands
-\def\languageshorthands#1{}
-$if(selnolig-langs)$
 \ifLuaTeX
-  \usepackage[$for(selnolig-langs)$$it$$sep$,$endfor$]{selnolig} % disable illegal ligatures
+  \usepackage{selnolig} % disable illegal ligatures
 \fi
 $endif$
-$endif$
 $--
 $-- pagestyle
 $--
diff --git a/src/resources/formats/beamer/pandoc/tables.tex b/src/resources/formats/beamer/pandoc/tables.tex
index c539bd640f9..443a14ab2f3 100644
--- a/src/resources/formats/beamer/pandoc/tables.tex
+++ b/src/resources/formats/beamer/pandoc/tables.tex
@@ -3,6 +3,7 @@
 $--
 $if(tables)$
 \usepackage{longtable,booktabs,array}
+\newcounter{none} % for unnumbered tables
 $if(multirow)$
 \usepackage{multirow}
 $endif$
diff --git a/src/resources/formats/jats/pandoc/default-templates/article.jats_publishing b/src/resources/formats/jats/pandoc/default-templates/article.jats_publishing
index d402b8bbd39..b33263cfd33 100644
--- a/src/resources/formats/jats/pandoc/default-templates/article.jats_publishing
+++ b/src/resources/formats/jats/pandoc/default-templates/article.jats_publishing
@@ -98,7 +98,7 @@ $if(author.surname)$
 <surname>$if(author.non-dropping-particle)$${author.non-dropping-particle} $endif$$author.surname$</surname>
 <given-names>$author.given-names$$if(author.dropping-particle)$ ${author.dropping-particle}$endif$</given-names>
 $if(author.prefix)$
-<prefix>${author.suffix}</prefix>
+<prefix>${author.prefix}</prefix>
 $endif$
 $if(author.suffix)$
 <suffix>${author.suffix}</suffix>
diff --git a/src/resources/formats/jats/pandoc/default-templates/default.jats_articleauthoring b/src/resources/formats/jats/pandoc/default-templates/default.jats_articleauthoring
index 627911ae516..5a4fa212872 100644
--- a/src/resources/formats/jats/pandoc/default-templates/default.jats_articleauthoring
+++ b/src/resources/formats/jats/pandoc/default-templates/default.jats_articleauthoring
@@ -31,7 +31,7 @@ $if(author.surname)$
 <surname>$if(author.non-dropping-particle)$${author.non-dropping-particle} $endif$${author.surname}</surname>
 <given-names>${author.given-names}$if(author.dropping-particle)$ ${author.dropping-particle}$endif$</given-names>
 $if(author.prefix)$
-<prefix>${author.suffix}</prefix>
+<prefix>${author.prefix}</prefix>
 $endif$
 $if(author.suffix)$
 <suffix>${author.suffix}</suffix>
diff --git a/src/resources/formats/pdf/pandoc/babel-lang.tex b/src/resources/formats/pdf/pandoc/babel-lang.tex
index f29c833cb1e..ad1cc90c499 100644
--- a/src/resources/formats/pdf/pandoc/babel-lang.tex
+++ b/src/resources/formats/pdf/pandoc/babel-lang.tex
@@ -3,9 +3,9 @@
 $--
 $if(lang)$
 \ifLuaTeX
-\usepackage[bidi=basic$for(babeloptions)$,$babeloptions$$endfor$]{babel}
+\usepackage[bidi=basic,shorthands=off,$for(babeloptions)$,$babeloptions$$endfor$]{babel}
 \else
-\usepackage[bidi=default$for(babeloptions)$,$babeloptions$$endfor$]{babel}
+\usepackage[bidi=default,shorthands=off,$for(babeloptions)$,$babeloptions$$endfor$]{babel}
 \fi
 $if(babel-lang)$
 $if(mainfont)$
@@ -18,12 +18,7 @@
 $for(babelfonts/pairs)$
 \babelfont[$babelfonts.key$]{rm}{$babelfonts.value$}
 $endfor$
-% get rid of language-specific shorthands (see #6817):
-\let\LanguageShortHands\languageshorthands
-\def\languageshorthands#1{}
-$if(selnolig-langs)$
 \ifLuaTeX
-  \usepackage[$for(selnolig-langs)$$it$$sep$,$endfor$]{selnolig} % disable illegal ligatures
+  \usepackage{selnolig} % disable illegal ligatures
 \fi
-$endif$
 $endif$
\ No newline at end of file
diff --git a/src/resources/formats/pdf/pandoc/latex.common b/src/resources/formats/pdf/pandoc/latex.common
index 3f93b1b883a..cb745941de6 100644
--- a/src/resources/formats/pdf/pandoc/latex.common
+++ b/src/resources/formats/pdf/pandoc/latex.common
@@ -183,9 +183,9 @@ $-- Babel language support
 $--
 $if(lang)$
 \ifLuaTeX
-\usepackage[bidi=basic$for(babeloptions)$,$babeloptions$$endfor$]{babel}
+\usepackage[bidi=basic,shorthands=off,$for(babeloptions)$,$babeloptions$$endfor$]{babel}
 \else
-\usepackage[bidi=default$for(babeloptions)$,$babeloptions$$endfor$]{babel}
+\usepackage[bidi=default,shorthands=off,$for(babeloptions)$,$babeloptions$$endfor$]{babel}
 \fi
 $if(babel-lang)$
 $if(mainfont)$
@@ -198,15 +198,10 @@ $endif$
 $for(babelfonts/pairs)$
 \babelfont[$babelfonts.key$]{rm}{$babelfonts.value$}
 $endfor$
-% get rid of language-specific shorthands (see #6817):
-\let\LanguageShortHands\languageshorthands
-\def\languageshorthands#1{}
-$if(selnolig-langs)$
 \ifLuaTeX
-  \usepackage[$for(selnolig-langs)$$it$$sep$,$endfor$]{selnolig} % disable illegal ligatures
+  \usepackage{selnolig} % disable illegal ligatures
 \fi
 $endif$
-$endif$
 $--
 $-- pagestyle
 $--
diff --git a/src/resources/formats/pdf/pandoc/tables.tex b/src/resources/formats/pdf/pandoc/tables.tex
index c539bd640f9..443a14ab2f3 100644
--- a/src/resources/formats/pdf/pandoc/tables.tex
+++ b/src/resources/formats/pdf/pandoc/tables.tex
@@ -3,6 +3,7 @@
 $--
 $if(tables)$
 \usepackage{longtable,booktabs,array}
+\newcounter{none} % for unnumbered tables
 $if(multirow)$
 \usepackage{multirow}
 $endif$
diff --git a/src/resources/formats/typst/pandoc/quarto/definitions.typ b/src/resources/formats/typst/pandoc/quarto/definitions.typ
index fff6dcdc4c1..c5b2f55e645 100644
--- a/src/resources/formats/typst/pandoc/quarto/definitions.typ
+++ b/src/resources/formats/typst/pandoc/quarto/definitions.typ
@@ -1,4 +1,16 @@
 // Some definitions presupposed by pandoc's typst output.
+#let content-to-string(content) = {
+  if content.has("text") {
+    content.text
+  } else if content.has("children") {
+    content.children.map(content-to-string).join("")
+  } else if content.has("body") {
+    content-to-string(content.body)
+  } else if content == [ ] {
+    " "
+  }
+}
+
 #let horizontalrule = line(start: (25%,0%), end: (75%,0%))
 
 #let endnote(num, contents) = [
@@ -171,3 +183,8 @@
     )
 }
 
+$if(highlighting-definitions)$
+// syntax highlighting functions from skylighting:
+$highlighting-definitions$
+
+$endif$
diff --git a/src/resources/formats/typst/pandoc/quarto/page.typ b/src/resources/formats/typst/pandoc/quarto/page.typ
index f5af676afdf..a0289428606 100644
--- a/src/resources/formats/typst/pandoc/quarto/page.typ
+++ b/src/resources/formats/typst/pandoc/quarto/page.typ
@@ -2,6 +2,7 @@
   paper: $if(papersize)$"$papersize$"$else$"us-letter"$endif$,
   margin: $if(margin)$($for(margin/pairs)$$margin.key$: $margin.value$,$endfor$)$else$(x: 1.25in, y: 1.25in)$endif$,
   numbering: $if(page-numbering)$"$page-numbering$"$else$none$endif$,
+  columns: $if(columns)$$columns$$else$1$endif$,
 )
 $if(logo)$
 #set page(background: align($logo.location$, box(inset: $logo.inset$, image("$logo.path$", width: $logo.width$$if(logo.alt)$, alt: "$logo.alt$"$endif$))))
diff --git a/src/resources/formats/typst/pandoc/quarto/typst-show.typ b/src/resources/formats/typst/pandoc/quarto/typst-show.typ
index 472e71c0c43..5c2d5fe86d5 100644
--- a/src/resources/formats/typst/pandoc/quarto/typst-show.typ
+++ b/src/resources/formats/typst/pandoc/quarto/typst-show.typ
@@ -61,6 +61,32 @@ $endif$
 $if(section-numbering)$
   sectionnumbering: "$section-numbering$",
 $endif$
+$if(mathfont)$
+  mathfont: ($for(mathfont)$"$mathfont$",$endfor$),
+$endif$
+$if(codefont)$
+  codefont: ($for(codefont)$"$codefont$",$endfor$),
+$elseif(brand.typography.monospace.family)$
+  codefont: $brand.typography.monospace.family$,
+$endif$
+$if(linestretch)$
+  linestretch: $linestretch$,
+$endif$
+$if(thanks)$
+  thanks: [$thanks$],
+$endif$
+$if(linkcolor)$
+  linkcolor: [$linkcolor$],
+$endif$
+$if(citecolor)$
+  citecolor: [$citecolor$],
+$endif$
+$if(filecolor)$
+  filecolor: [$filecolor$],
+$endif$
+$if(keywords)$
+  keywords: ($for(keywords)$"$keywords$",$endfor$),
+$endif$
 $if(toc)$
   toc: $toc$,
 $endif$
diff --git a/src/resources/formats/typst/pandoc/quarto/typst-template.typ b/src/resources/formats/typst/pandoc/quarto/typst-template.typ
index 02c0dc041e1..34becf2872f 100644
--- a/src/resources/formats/typst/pandoc/quarto/typst-template.typ
+++ b/src/resources/formats/typst/pandoc/quarto/typst-template.typ
@@ -1,85 +1,114 @@
 
-
 #let article(
   title: none,
   subtitle: none,
   authors: none,
+  keywords: (),
   date: none,
-  abstract: none,
   abstract-title: none,
+  abstract: none,
+  thanks: none,
   cols: 1,
   lang: "en",
   region: "US",
-  font: "libertinus serif",
+  font: none,
   fontsize: 11pt,
   title-size: 1.5em,
   subtitle-size: 1.25em,
-  heading-family: "libertinus serif",
+  heading-family: none,
   heading-weight: "bold",
   heading-style: "normal",
   heading-color: black,
   heading-line-height: 0.65em,
+  mathfont: none,
+  codefont: none,
+  linestretch: 1,
   sectionnumbering: none,
+  linkcolor: none,
+  citecolor: none,
+  filecolor: none,
   toc: false,
   toc_title: none,
   toc_depth: none,
   toc_indent: 1.5em,
   doc,
 ) = {
-  set par(justify: true)
+  // Set document metadata for PDF accessibility
+  set document(title: title, keywords: keywords)
+  set document(
+    author: authors.map(author => content-to-string(author.name)).join(", ", last: " & "),
+  ) if authors != none and authors != ()
+  set par(
+    justify: true,
+    leading: linestretch * 0.65em
+  )
   set text(lang: lang,
            region: region,
-           font: font,
            size: fontsize)
+  set text(font: font) if font != none
+  show math.equation: set text(font: mathfont) if mathfont != none
+  show raw: set text(font: codefont) if codefont != none
+
   set heading(numbering: sectionnumbering)
-  if title != none {
-    align(center)[#block(inset: 2em)[
-      #set par(leading: heading-line-height)
-      #if (heading-family != none or heading-weight != "bold" or heading-style != "normal"
-           or heading-color != black) {
-        set text(font: heading-family, weight: heading-weight, style: heading-style, fill: heading-color)
-        text(size: title-size)[#title]
-        if subtitle != none {
+
+  show link: set text(fill: rgb(content-to-string(linkcolor))) if linkcolor != none
+  show ref: set text(fill: rgb(content-to-string(citecolor))) if citecolor != none
+  show link: this => {
+    if filecolor != none and type(this.dest) == label {
+      text(this, fill: rgb(content-to-string(filecolor)))
+    } else {
+      text(this)
+    }
+   }
+
+  block(below: 1em, width: 100%)[
+    #if title != none {
+      align(center, block(inset: 2em)[
+        #set par(leading: heading-line-height) if heading-line-height != none
+        #set text(font: heading-family) if heading-family != none
+        #set text(weight: heading-weight)
+        #set text(style: heading-style) if heading-style != "normal"
+        #set text(fill: heading-color) if heading-color != black
+
+        #text(size: title-size)[#title #if thanks != none {
+          footnote(thanks, numbering: "*")
+          counter(footnote).update(n => n - 1)
+        }]
+        #(if subtitle != none {
           parbreak()
           text(size: subtitle-size)[#subtitle]
-        }
-      } else {
-        text(weight: "bold", size: title-size)[#title]
-        if subtitle != none {
-          parbreak()
-          text(weight: "bold", size: subtitle-size)[#subtitle]
-        }
-      }
-    ]]
-  }
+        })
+      ])
+    }
 
-  if authors != none {
-    let count = authors.len()
-    let ncols = calc.min(count, 3)
-    grid(
-      columns: (1fr,) * ncols,
-      row-gutter: 1.5em,
-      ..authors.map(author =>
-          align(center)[
-            #author.name \
-            #author.affiliation \
-            #author.email
-          ]
+    #if authors != none and authors != () {
+      let count = authors.len()
+      let ncols = calc.min(count, 3)
+      grid(
+        columns: (1fr,) * ncols,
+        row-gutter: 1.5em,
+        ..authors.map(author =>
+            align(center)[
+              #author.name \
+              #author.affiliation \
+              #author.email
+            ]
+        )
       )
-    )
-  }
+    }
 
-  if date != none {
-    align(center)[#block(inset: 1em)[
-      #date
-    ]]
-  }
+    #if date != none {
+      align(center)[#block(inset: 1em)[
+        #date
+      ]]
+    }
 
-  if abstract != none {
-    block(inset: 2em)[
-    #text(weight: "semibold")[#abstract-title] #h(1em) #abstract
-    ]
-  }
+    #if abstract != none {
+      block(inset: 2em)[
+      #text(weight: "semibold")[#abstract-title] #h(1em) #abstract
+      ]
+    }
+  ]
 
   if toc {
     let title = if toc_title == none {
diff --git a/src/resources/formats/typst/pandoc/template.typst b/src/resources/formats/typst/pandoc/template.typst
index 1889bef6fa5..648476620f5 100644
--- a/src/resources/formats/typst/pandoc/template.typst
+++ b/src/resources/formats/typst/pandoc/template.typst
@@ -15,74 +15,104 @@
   authors: (),
   keywords: (),
   date: none,
+  abstract-title: none,
   abstract: none,
+  thanks: none,
   cols: 1,
   margin: (x: 1.25in, y: 1.25in),
   paper: "us-letter",
   lang: "en",
   region: "US",
-  font: (),
+  font: none,
   fontsize: 11pt,
+  mathfont: none,
+  codefont: none,
+  linestretch: 1,
   sectionnumbering: none,
+  linkcolor: none,
+  citecolor: none,
+  filecolor: none,
   pagenumbering: "1",
   doc,
 ) = {
   set document(
     title: title,
-    author: authors.map(author => content-to-string(author.name)),
     keywords: keywords,
   )
+  set document(
+      author: authors.map(author => content-to-string(author.name)).join(", ", last: " & "),
+  ) if authors != none and authors != ()
   set page(
     paper: paper,
     margin: margin,
     numbering: pagenumbering,
-    columns: cols,
-    )
-  set par(justify: true)
+    columns: cols
+  )
+
+  set par(
+    justify: true,
+    leading: linestretch * 0.65em
+  )
   set text(lang: lang,
            region: region,
-           font: font,
            size: fontsize)
+
+  set text(font: font) if font != none
+  show math.equation: set text(font: mathfont) if mathfont != none
+  show raw: set text(font: codefont) if codefont != none
+
   set heading(numbering: sectionnumbering)
 
-  place(top, float: true, scope: "parent", clearance: 4mm)[
-  #if title != none {
-    align(center)[#block(inset: 2em)[
-      #text(weight: "bold", size: 1.5em)[#title]
-      #(if subtitle != none {
-        parbreak()
-        text(weight: "bold", size: 1.25em)[#subtitle]
-      })
-    ]]
+  show link: set text(fill: rgb(content-to-string(linkcolor))) if linkcolor != none
+  show ref: set text(fill: rgb(content-to-string(citecolor))) if citecolor != none
+  show link: this => {
+    if filecolor != none and type(this.dest) == label {
+      text(this, fill: rgb(content-to-string(filecolor)))
+    } else {
+      text(this)
+    }
   }
 
-  #if authors != none and authors != [] {
-    let count = authors.len()
-    let ncols = calc.min(count, 3)
-    grid(
-      columns: (1fr,) * ncols,
-      row-gutter: 1.5em,
-      ..authors.map(author =>
-          align(center)[
-            #author.name \
-            #author.affiliation \
-            #author.email
-          ]
+  block(below: 1em, width: 100%)[
+    #if title != none {
+      align(center, block[
+          #text(weight: "bold", size: 1.5em)[#title #if thanks != none {
+              footnote(thanks, numbering: "*")
+              counter(footnote).update(n => n - 1)
+            }]
+          #(
+            if subtitle != none {
+              parbreak()
+              text(weight: "bold", size: 1.25em)[#subtitle]
+            }
+           )])
+    }
+
+    #if authors != none and authors != [] {
+      let count = authors.len()
+      let ncols = calc.min(count, 3)
+      grid(
+        columns: (1fr,) * ncols,
+        row-gutter: 1.5em,
+        ..authors.map(author => align(center)[
+          #author.name \
+          #author.affiliation \
+          #author.email
+        ])
       )
-    )
-  }
+    }
 
-  #if date != none {
-    align(center)[#block(inset: 1em)[
-      #date
-    ]]
-  }
+    #if date != none {
+      align(center)[#block(inset: 1em)[
+          #date
+        ]]
+    }
 
-  #if abstract != none {
-    block(inset: 2em)[
-    #text(weight: "semibold")[Abstract] #h(1em) #abstract
-    ]
-  }
+    #if abstract != none {
+      block(inset: 2em)[
+        #text(weight: "semibold")[#abstract-title] #h(1em) #abstract
+      ]
+    }
   ]
 
   doc
diff --git a/src/resources/formats/typst/pandoc/typst.template b/src/resources/formats/typst/pandoc/typst.template
index 79b2c33f583..a499cd8db9f 100644
--- a/src/resources/formats/typst/pandoc/typst.template
+++ b/src/resources/formats/typst/pandoc/typst.template
@@ -22,6 +22,11 @@
   kind: image
 ): set figure.caption(position: $if(figure-caption-position)$$figure-caption-position$$else$bottom$endif$)
 
+$if(highlighting-definitions)$
+// syntax highlighting functions from skylighting:
+$highlighting-definitions$
+
+$endif$
 $if(template)$
 #import "$template$": conf
 $else$
@@ -60,7 +65,7 @@ $endfor$
     ),
 $endif$
 $if(keywords)$
-  keywords: ($for(keywords)$$keyword$$sep$,$endfor$),
+  keywords: ($for(keywords)$$keywords$$sep$,$endfor$),
 $endif$
 $if(date)$
   date: [$date$],
@@ -71,9 +76,15 @@ $endif$
 $if(region)$
   region: "$region$",
 $endif$
+$if(abstract-title)$
+  abstract-title: [$abstract-title$],
+$endif$
 $if(abstract)$
   abstract: [$abstract$],
 $endif$
+$if(thanks)$
+  thanks: [$thanks$],
+$endif$
 $if(margin)$
   margin: ($for(margin/pairs)$$margin.key$: $margin.value$,$endfor$),
 $endif$
@@ -86,10 +97,28 @@ $endif$
 $if(fontsize)$
   fontsize: $fontsize$,
 $endif$
+$if(mathfont)$
+  mathfont: ($for(mathfont)$"$mathfont$",$endfor$),
+$endif$
+$if(codefont)$
+  codefont: ($for(codefont)$"$codefont$",$endfor$),
+$endif$
+$if(linestretch)$
+  linestretch: $linestretch$,
+$endif$
 $if(section-numbering)$
   sectionnumbering: "$section-numbering$",
 $endif$
   pagenumbering: $if(page-numbering)$"$page-numbering$"$else$none$endif$,
+$if(linkcolor)$
+  linkcolor: [$linkcolor$],
+$endif$
+$if(citecolor)$
+  citecolor: [$citecolor$],
+$endif$
+$if(filecolor)$
+  filecolor: [$filecolor$],
+$endif$
   cols: $if(columns)$$columns$$else$1$endif$,
   doc,
 )
@@ -108,6 +137,9 @@ $endif$
 $body$
 
 $if(citations)$
+$for(nocite-ids)$
+#cite(label("${it}"), form: none)
+$endfor$
 $if(csl)$
 
 #set bibliography(style: "$csl$")
@@ -117,7 +149,7 @@ $elseif(bibliographystyle)$
 $endif$
 $if(bibliography)$
 
-#bibliography($for(bibliography)$"$bibliography$"$sep$,$endfor$)
+#bibliography(($for(bibliography)$"$bibliography$"$sep$,$endfor$)$if(full-bibliography)$, full: true$endif$)
 $endif$
 $endif$
 $for(include-after)$
diff --git a/tests/docs/smoke-all/typst/brand-yaml/typography/font-list.qmd b/tests/docs/smoke-all/typst/brand-yaml/typography/font-list.qmd
index 4b76245b8ac..968ea05845e 100644
--- a/tests/docs/smoke-all/typst/brand-yaml/typography/font-list.qmd
+++ b/tests/docs/smoke-all/typst/brand-yaml/typography/font-list.qmd
@@ -20,8 +20,8 @@ _quarto:
       ensureTypstFileRegexMatches:
         -
           - 'font: \("InvalidFont", "Roboto"\),'
-          - '#show raw.where\(block: false\): set text\(font: \("InvalidFont", "Inconsolata"\), \)'
-          - '#show raw.where\(block: true\): set text\(font: \("InvalidFont", "Inconsolata"\), \)'
+          # monospace font now goes through codefont parameter instead of header injection
+          - 'codefont: \("InvalidFont", "Inconsolata"\),'
         - []
       ensurePdfRegexMatches:
         -
diff --git a/tests/docs/smoke-all/typst/brand-yaml/typography/kitchen-sink-1/.quarto/typst-font-cache/fonts.gstatic.com/s/aguafinascript/v24/If2QXTv_ZzSxGIO30LemWEOmt1b3rcQt.ttf b/tests/docs/smoke-all/typst/brand-yaml/typography/kitchen-sink-1/.quarto/typst-font-cache/fonts.gstatic.com/s/aguafinascript/v24/If2QXTv_ZzSxGIO30LemWEOmt1b3rcQt.ttf
new file mode 100644
index 00000000000..7f546f35ccd
Binary files /dev/null and b/tests/docs/smoke-all/typst/brand-yaml/typography/kitchen-sink-1/.quarto/typst-font-cache/fonts.gstatic.com/s/aguafinascript/v24/If2QXTv_ZzSxGIO30LemWEOmt1b3rcQt.ttf differ
diff --git a/tests/docs/smoke-all/typst/brand-yaml/typography/kitchen-sink-1/.quarto/typst-font-cache/fonts.gstatic.com/s/inconsolata/v37/QldgNThLqRwH-OJ1UHjlKENVzkWGVkL3GZQmAwLYxYWI2qfdm7Lpp1s7WR32kg.ttf b/tests/docs/smoke-all/typst/brand-yaml/typography/kitchen-sink-1/.quarto/typst-font-cache/fonts.gstatic.com/s/inconsolata/v37/QldgNThLqRwH-OJ1UHjlKENVzkWGVkL3GZQmAwLYxYWI2qfdm7Lpp1s7WR32kg.ttf
new file mode 100644
index 00000000000..16c32c75b10
Binary files /dev/null and b/tests/docs/smoke-all/typst/brand-yaml/typography/kitchen-sink-1/.quarto/typst-font-cache/fonts.gstatic.com/s/inconsolata/v37/QldgNThLqRwH-OJ1UHjlKENVzkWGVkL3GZQmAwLYxYWI2qfdm7Lpp1s7WR32kg.ttf differ
diff --git a/tests/docs/smoke-all/typst/brand-yaml/typography/kitchen-sink-1/.quarto/typst-font-cache/fonts.gstatic.com/s/inconsolata/v37/QldgNThLqRwH-OJ1UHjlKENVzkWGVkL3GZQmAwLYxYWI2qfdm7Lpp4U8WR32kg.ttf b/tests/docs/smoke-all/typst/brand-yaml/typography/kitchen-sink-1/.quarto/typst-font-cache/fonts.gstatic.com/s/inconsolata/v37/QldgNThLqRwH-OJ1UHjlKENVzkWGVkL3GZQmAwLYxYWI2qfdm7Lpp4U8WR32kg.ttf
new file mode 100644
index 00000000000..f81dccc97d9
Binary files /dev/null and b/tests/docs/smoke-all/typst/brand-yaml/typography/kitchen-sink-1/.quarto/typst-font-cache/fonts.gstatic.com/s/inconsolata/v37/QldgNThLqRwH-OJ1UHjlKENVzkWGVkL3GZQmAwLYxYWI2qfdm7Lpp4U8WR32kg.ttf differ
diff --git a/tests/docs/smoke-all/typst/brand-yaml/typography/kitchen-sink-1/.quarto/typst-font-cache/fonts.gstatic.com/s/montserrat/v31/JTUFjIg1_i6t8kCHKm459Wx7xQYXK0vOoz6jq6R9WXh0ow.ttf b/tests/docs/smoke-all/typst/brand-yaml/typography/kitchen-sink-1/.quarto/typst-font-cache/fonts.gstatic.com/s/montserrat/v31/JTUFjIg1_i6t8kCHKm459Wx7xQYXK0vOoz6jq6R9WXh0ow.ttf
new file mode 100644
index 00000000000..1aee202a63a
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diff --git a/tests/docs/smoke-all/typst/brand-yaml/typography/kitchen-sink-1/.quarto/typst-font-cache/fonts.gstatic.com/s/robotoslab/v36/BngbUXZYTXPIvIBgJJSb6s3BzlRRfKOFbvjojISmb2Rm.ttf b/tests/docs/smoke-all/typst/brand-yaml/typography/kitchen-sink-1/.quarto/typst-font-cache/fonts.gstatic.com/s/robotoslab/v36/BngbUXZYTXPIvIBgJJSb6s3BzlRRfKOFbvjojISmb2Rm.ttf
new file mode 100644
index 00000000000..9fc573f0c35
Binary files /dev/null and b/tests/docs/smoke-all/typst/brand-yaml/typography/kitchen-sink-1/.quarto/typst-font-cache/fonts.gstatic.com/s/robotoslab/v36/BngbUXZYTXPIvIBgJJSb6s3BzlRRfKOFbvjojISmb2Rm.ttf differ
diff --git a/tests/docs/smoke-all/typst/brand-yaml/typography/kitchen-sink-1/brand-typography.qmd b/tests/docs/smoke-all/typst/brand-yaml/typography/kitchen-sink-1/brand-typography.qmd
index 23ce2483fed..6912828f2d4 100644
--- a/tests/docs/smoke-all/typst/brand-yaml/typography/kitchen-sink-1/brand-typography.qmd
+++ b/tests/docs/smoke-all/typst/brand-yaml/typography/kitchen-sink-1/brand-typography.qmd
@@ -35,10 +35,12 @@ _quarto:
         - '^#show heading: set text\(font: \("Montserrat",\), weight: 800, style: "normal", fill: rgb\("#0b8005"\), \)$'
         - '^#show heading: set par\(leading: 0.25em\)$'
 
-        - '^#show raw.where\(block: false\): set text\(font: \("Inconsolata",\), weight: 600, size: 0.57\*14pt, fill: rgb\(8, 111, 15\), \)$'
+        - 'codefont: \("Inconsolata",\),$'
+        - 'show raw: set text\(font: codefont\) if codefont != none'
+        - '^#show raw.where\(block: false\): set text\(weight: 600, size: 0.57\*14pt, fill: rgb\(8, 111, 15\), \)$'
         - '^#show raw.where\(block: false\): content => highlight\(fill: rgb\(255, 250, 224\), content\)$'
 
-        - '^#show raw.where\(block: true\): set text\(font: \("Inconsolata",\), size: 18pt, fill: rgb\(245, 255, 250\), \)$'
+        - '^#show raw.where\(block: true\): set text\(size: 18pt, fill: rgb\(245, 255, 250\), \)$'
         - '^#show raw.where\(block: true\): set block\(fill: rgb\("#77aae1"\)\)$'
         - '^#show raw.where\(block: true\): set par\(leading: 1\.25em\)$'
 
diff --git a/tests/docs/smoke-all/typst/brand-yaml/typography/kitchen-sink-2/.quarto/typst-font-cache/fonts.gstatic.com/s/ebgaramond/v32/SlGDmQSNjdsmc35JDF1K5E55YMjF_7DPuGi-6_RkBI96.ttf b/tests/docs/smoke-all/typst/brand-yaml/typography/kitchen-sink-2/.quarto/typst-font-cache/fonts.gstatic.com/s/ebgaramond/v32/SlGDmQSNjdsmc35JDF1K5E55YMjF_7DPuGi-6_RkBI96.ttf
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diff --git a/tests/docs/smoke-all/typst/brand-yaml/typography/kitchen-sink-2/.quarto/typst-font-cache/fonts.gstatic.com/s/ebgaramond/v32/SlGFmQSNjdsmc35JDF1K5GRwUjcdlttVFm-rI7e8QL99U60.ttf b/tests/docs/smoke-all/typst/brand-yaml/typography/kitchen-sink-2/.quarto/typst-font-cache/fonts.gstatic.com/s/ebgaramond/v32/SlGFmQSNjdsmc35JDF1K5GRwUjcdlttVFm-rI7e8QL99U60.ttf
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diff --git a/tests/docs/smoke-all/typst/brand-yaml/typography/kitchen-sink-2/.quarto/typst-font-cache/fonts.gstatic.com/s/gentiumplus/v2/IurD6Ytw-oSPaZ00r2bNe8VZjqFPwGw.ttf b/tests/docs/smoke-all/typst/brand-yaml/typography/kitchen-sink-2/.quarto/typst-font-cache/fonts.gstatic.com/s/gentiumplus/v2/IurD6Ytw-oSPaZ00r2bNe8VZjqFPwGw.ttf
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diff --git a/tests/docs/smoke-all/typst/brand-yaml/typography/kitchen-sink-2/.quarto/typst-font-cache/fonts.gstatic.com/s/gentiumplus/v2/Iurd6Ytw-oSPaZ00r2bNe8VZi5FI.ttf b/tests/docs/smoke-all/typst/brand-yaml/typography/kitchen-sink-2/.quarto/typst-font-cache/fonts.gstatic.com/s/gentiumplus/v2/Iurd6Ytw-oSPaZ00r2bNe8VZi5FI.ttf
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diff --git a/tests/docs/smoke-all/typst/brand-yaml/typography/kitchen-sink-2/.quarto/typst-font-cache/fonts.gstatic.com/s/raleway/v37/1Pt_g8zYS_SKggPNyCgSQamb1W0lwk4S4WjMDrMfJQ.ttf b/tests/docs/smoke-all/typst/brand-yaml/typography/kitchen-sink-2/.quarto/typst-font-cache/fonts.gstatic.com/s/raleway/v37/1Pt_g8zYS_SKggPNyCgSQamb1W0lwk4S4WjMDrMfJQ.ttf
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diff --git a/tests/docs/smoke-all/typst/brand-yaml/typography/kitchen-sink-2/.quarto/typst-font-cache/fonts.gstatic.com/s/raleway/v37/1Ptxg8zYS_SKggPN4iEgvnHyvveLxVvaorCIPrQ.ttf b/tests/docs/smoke-all/typst/brand-yaml/typography/kitchen-sink-2/.quarto/typst-font-cache/fonts.gstatic.com/s/raleway/v37/1Ptxg8zYS_SKggPN4iEgvnHyvveLxVvaorCIPrQ.ttf
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diff --git a/tests/docs/smoke-all/typst/brand-yaml/typography/kitchen-sink-2/.quarto/typst-font-cache/fonts.gstatic.com/s/spacemono/v17/i7dNIFZifjKcF5UAWdDRYERMR3K6.ttf b/tests/docs/smoke-all/typst/brand-yaml/typography/kitchen-sink-2/.quarto/typst-font-cache/fonts.gstatic.com/s/spacemono/v17/i7dNIFZifjKcF5UAWdDRYERMR3K6.ttf
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diff --git a/tests/docs/smoke-all/typst/brand-yaml/typography/kitchen-sink-2/.quarto/typst-font-cache/fonts.gstatic.com/s/spacemono/v17/i7dPIFZifjKcF5UAWdDRYEF8QA.ttf b/tests/docs/smoke-all/typst/brand-yaml/typography/kitchen-sink-2/.quarto/typst-font-cache/fonts.gstatic.com/s/spacemono/v17/i7dPIFZifjKcF5UAWdDRYEF8QA.ttf
new file mode 100644
index 00000000000..6ccee6c1963
Binary files /dev/null and b/tests/docs/smoke-all/typst/brand-yaml/typography/kitchen-sink-2/.quarto/typst-font-cache/fonts.gstatic.com/s/spacemono/v17/i7dPIFZifjKcF5UAWdDRYEF8QA.ttf differ
diff --git a/tests/docs/smoke-all/typst/brand-yaml/typography/kitchen-sink-2/brand-typography.qmd b/tests/docs/smoke-all/typst/brand-yaml/typography/kitchen-sink-2/brand-typography.qmd
index bbac8f51ce5..3f59bd8747e 100644
--- a/tests/docs/smoke-all/typst/brand-yaml/typography/kitchen-sink-2/brand-typography.qmd
+++ b/tests/docs/smoke-all/typst/brand-yaml/typography/kitchen-sink-2/brand-typography.qmd
@@ -33,10 +33,12 @@ _quarto:
         - '^#show heading: set text\(font: \("Raleway",\), weight: 500, style: "normal", fill: rgb\("#042f02"\), \)$'
         - '^#show heading: set par\(leading: 0.25em\)$'
 
-        - '^#show raw.where\(block: false\): set text\(font: \("Space Mono",\), weight: 400, size: 0.75\*12pt, fill: rgb\(8, 111, 15\), \)$'
+        - 'codefont: \("Space Mono",\),$'
+        - 'show raw: set text\(font: codefont\) if codefont != none'
+        - '^#show raw.where\(block: false\): set text\(weight: 400, size: 0.75\*12pt, fill: rgb\(8, 111, 15\), \)$'
         - '^#show raw.where\(block: false\): content => highlight\(fill: rgb\(255, 250, 224\), content\)$'
 
-        - '^#show raw.where\(block: true\): set text\(font: \("Space Mono",\), weight: 400, size: 0.75\*12pt, fill: rgb\("#eee"\), \)$'
+        - '^#show raw.where\(block: true\): set text\(weight: 400, size: 0.75\*12pt, fill: rgb\("#eee"\), \)$'
         - '^#show raw.where\(block: true\): set block\(fill: rgb\("#0a3c07"\)\)$'
 
         - '^#show link: set text\(weight: 200, fill: maroon, \)$'
diff --git a/tests/docs/smoke-all/typst/pandoc-template-features.qmd b/tests/docs/smoke-all/typst/pandoc-template-features.qmd
new file mode 100644
index 00000000000..479bf4a3e4b
--- /dev/null
+++ b/tests/docs/smoke-all/typst/pandoc-template-features.qmd
@@ -0,0 +1,96 @@
+---
+title: "Test Document"
+subtitle: "Pandoc Template Features"
+author:
+  - name: Alice Smith
+    email: alice@example.com
+    affiliation: University A
+  - name: Bob Jones
+    email: bob@example.com
+    affiliation: University B
+date: "2024-01-15"
+keywords:
+  - quarto
+  - typst
+  - testing
+thanks: "We thank our reviewers for their feedback."
+abstract: "This document tests the Pandoc typst template features merged into Quarto."
+mainfont: "Libertinus Serif"
+mathfont: "STIX Two Math"
+linestretch: 1.2
+linkcolor: "#0000ff"
+citecolor: "#00ff00"
+filecolor: "#ff0000"
+brand:
+  typography:
+    fonts:
+      - family: Fira Code
+        source: google
+    monospace:
+      family: Fira Code
+format:
+  typst:
+    keep-typ: true
+_quarto:
+  tests:
+    typst:
+      ensureTypstFileRegexMatches:
+        - # Patterns that MUST be found
+          # content-to-string function defined (from Pandoc)
+          - '#let content-to-string\(content\)'
+          # Document metadata in article() function
+          - 'set document\(title: title, keywords: keywords\)'
+          - 'set document\(\s*author: authors\.map'
+          # Keywords passed to article() call (quoted strings)
+          - 'keywords: \("quarto","typst","testing",\)'
+          # Thanks parameter passed to article()
+          - 'thanks: \[We thank our reviewers'
+          # Thanks footnote in title block
+          - 'footnote\(thanks, numbering: "\*"\)'
+          # Font settings passed to article()
+          # codefont comes from brand.typography.monospace.family fallback
+          - 'codefont: \("Fira Code",\)'
+          - 'mathfont: \("STIX Two Math",\)'
+          # mainfont (Libertinus Serif is bundled with Typst)
+          - 'font: \("Libertinus Serif",\)'
+          # Linestretch
+          - 'linestretch: 1\.2'
+          # Link colors passed to article() (# escaped as \#)
+          - 'linkcolor: \[\\#0000ff\]'
+          - 'citecolor: \[\\#00ff00\]'
+          - 'filecolor: \[\\#ff0000\]'
+          # Link color show rules in article() function
+          - 'show link: set text\(fill: rgb\(content-to-string\(linkcolor\)\)\)'
+          - 'show ref: set text\(fill: rgb\(content-to-string\(citecolor\)\)\)'
+        - # Patterns that must NOT be found
+          []
+---
+
+## Introduction
+
+This document tests all the Pandoc typst template features that have been merged into Quarto's modular template structure.
+
+## Code Example
+
+Here is some code with custom font:
+
+```python
+def hello():
+    print("Hello, world!")
+```
+
+## Math Example
+
+Here is some math with custom font:
+
+$$
+E = mc^2
+$$
+
+## Links
+
+Here is a [link to Quarto](https://quarto.org) which should be colored.
+
+## Conclusion
+
+All features work correctly.
diff --git a/tests/docs/websites/website-sidebar-auto/.gitignore b/tests/docs/websites/website-sidebar-auto/.gitignore
new file mode 100644
index 00000000000..b5d6aa19d53
--- /dev/null
+++ b/tests/docs/websites/website-sidebar-auto/.gitignore
@@ -0,0 +1,4 @@
+/.quarto/
+**/*.quarto_ipynb
+*_files/
+_site/
diff --git a/tests/docs/websites/website-sidebar-auto/_quarto.yml b/tests/docs/websites/website-sidebar-auto/_quarto.yml
new file mode 100644
index 00000000000..a743825dfdd
--- /dev/null
+++ b/tests/docs/websites/website-sidebar-auto/_quarto.yml
@@ -0,0 +1,11 @@
+project:
+  type: website
+
+website:
+  title: "Sidebar Auto Test"
+  sidebar:
+    contents: auto
+
+format:
+  html:
+    theme: default
diff --git a/tests/docs/websites/website-sidebar-auto/index.qmd b/tests/docs/websites/website-sidebar-auto/index.qmd
new file mode 100644
index 00000000000..50187e5080c
--- /dev/null
+++ b/tests/docs/websites/website-sidebar-auto/index.qmd
@@ -0,0 +1,5 @@
+---
+title: "Home"
+---
+
+This is the home page.
diff --git a/tests/docs/websites/website-sidebar-auto/subdir/index.ipynb b/tests/docs/websites/website-sidebar-auto/subdir/index.ipynb
new file mode 100644
index 00000000000..b03257b03b3
--- /dev/null
+++ b/tests/docs/websites/website-sidebar-auto/subdir/index.ipynb
@@ -0,0 +1,33 @@
+{
+  "cells": [
+    {
+      "cell_type": "raw",
+      "metadata": {},
+      "source": [
+        "---\n",
+        "title: \"Subdir Index\"\n",
+        "---"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "This is the index page for the subdir."
+      ]
+    }
+  ],
+  "metadata": {
+    "kernelspec": {
+      "display_name": "Python 3",
+      "language": "python",
+      "name": "python3"
+    },
+    "language_info": {
+      "name": "python",
+      "version": "3.9.0"
+    }
+  },
+  "nbformat": 4,
+  "nbformat_minor": 4
+}
diff --git a/tests/smoke/website/website-sidebar-auto.test.ts b/tests/smoke/website/website-sidebar-auto.test.ts
new file mode 100644
index 00000000000..236d0e70776
--- /dev/null
+++ b/tests/smoke/website/website-sidebar-auto.test.ts
@@ -0,0 +1,37 @@
+/*
+ * website-sidebar-auto.test.ts
+ *
+ * Verifies that sidebar auto-generation properly detects index files with
+ * non-qmd extensions (like .ipynb) in subdirectories. This tests the
+ * engineValidExtensions() call in indexFileHrefForDir() which must work
+ * before resolveEngines() has been called.
+ *
+ * Copyright (C) 2020-2025 Posit Software, PBC
+ */
+
+import { docs } from "../../utils.ts";
+import { join } from "../../../src/deno_ral/path.ts";
+import { existsSync } from "../../../src/deno_ral/fs.ts";
+import { testQuartoCmd } from "../../test.ts";
+import { fileExists, noErrorsOrWarnings } from "../../verify.ts";
+
+const renderDir = docs("websites/website-sidebar-auto");
+const outDir = join(Deno.cwd(), renderDir, "_site");
+
+// Test that sidebar auto-generation detects index.ipynb in subdirectory
+testQuartoCmd(
+  "render",
+  [renderDir],
+  [
+    noErrorsOrWarnings,
+    fileExists(join(outDir, "index.html")),              // Main index page
+    fileExists(join(outDir, "subdir", "index.html")),    // Subdir index from .ipynb should be rendered
+  ],
+  {
+    teardown: async () => {
+      if (existsSync(outDir)) {
+        await Deno.remove(outDir, { recursive: true });
+      }
+    },
+  },
+);