From ff7843d3ae5db19aa5bef5c0ee8e467e9fac77a8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Micka=C3=ABl=20Canouil?=
 <8896044+mcanouil@users.noreply.github.com>
Date: Tue, 24 Mar 2026 15:49:59 +0100
Subject: [PATCH 1/8] fix: neutralise inline code in title scaffolds for Typst
 output

Quarto wraps theorem/example titles in __quarto_custom_scaffold Divs
with inline-only content. Both the code-window box wrapping and Pandoc's
Skylighting generate Typst function calls (#box(...), #NormalTok(...))
that get stringified as literal text when Quarto renders the title
parameter as a string.

Replace the global Code filter with a selective document walk that
converts Code to plain Typst backtick code inside title scaffolds and
applies the full box styling everywhere else.
---
 CHANGELOG.md                                  |  1 +
 .../_modules/hotfix/skylighting-typst-fix.lua | 62 +++++++++++++++++--
 2 files changed, 58 insertions(+), 5 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7d903ca..f0e3fd6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,7 @@
 ### Bug Fixes
 
 - fix: unwrap Quarto's `DecoratedCodeBlock` Div to prevent double filename wrapping in Typst output.
+- fix: prevent inline code in theorem/example titles from being converted to raw Typst markup that gets stringified.
 - fix: normalise code blocks with no or unknown language class to `default` for consistent styling across all formats.
 - fix: default to `#` comment symbol for unknown code block languages (`default`, `txt`, etc.) in annotation detection.
 - fix: support code annotations with `syntax-highlighting: idiomatic` (native Typst highlighting) via a `show raw.line` rule.
diff --git a/_extensions/code-window/_modules/hotfix/skylighting-typst-fix.lua b/_extensions/code-window/_modules/hotfix/skylighting-typst-fix.lua
index b63fb13..251766e 100644
--- a/_extensions/code-window/_modules/hotfix/skylighting-typst-fix.lua
+++ b/_extensions/code-window/_modules/hotfix/skylighting-typst-fix.lua
@@ -218,18 +218,70 @@ function Pandoc(doc)
   return doc
 end
 
---- Wrap inline Code elements with a background box in Typst output.
-function Code(el)
+--- Check if a Div is a Quarto title scaffold (inline-only content).
+--- Quarto wraps theorem/example titles in __quarto_custom_scaffold Divs
+--- containing a single Plain or Para block. Converting Code to RawInline
+--- inside these Divs causes the raw Typst markup to be stringified as
+--- literal text in the title parameter.
+--- @param div pandoc.Div
+--- @return boolean
+local function is_title_scaffold(div)
+  if div.attributes['__quarto_custom_scaffold'] ~= 'true' then
+    return false
+  end
+  for _, child in ipairs(div.content) do
+    if child.t ~= 'Plain' and child.t ~= 'Para' then
+      return false
+    end
+  end
+  return true
+end
+
+--- Convert Code to plain Typst backtick code inside title scaffolds.
+--- Prevents both the code-window box wrapping AND Pandoc's Skylighting
+--- from generating Typst function calls that get stringified by Quarto.
+--- @param el pandoc.Code
+--- @return pandoc.RawInline
+local function neutralise_title_code(el)
+  return pandoc.RawInline('typst', '`' .. el.text .. '`')
+end
+
+--- Walk the document tree and convert inline Code to RawInline with
+--- background styling, skipping title scaffolds where the conversion
+--- would produce raw Typst markup that gets stringified by Quarto.
+local function process_inline_code(doc)
   if not quarto.doc.is_format('typst') then
-    return el
+    return doc
   end
-  return process_typst_inline(el)
+
+  local code_filter = { Code = function(el) return process_typst_inline(el) end }
+  local title_filter = { Code = neutralise_title_code }
+
+  local function walk_blocks(blocks)
+    local new_blocks = {}
+    for _, blk in ipairs(blocks) do
+      if blk.t == 'Div' then
+        if is_title_scaffold(blk) then
+          table.insert(new_blocks, blk:walk(title_filter))
+        else
+          blk.content = walk_blocks(blk.content)
+          table.insert(new_blocks, blk)
+        end
+      else
+        table.insert(new_blocks, blk:walk(code_filter))
+      end
+    end
+    return pandoc.Blocks(new_blocks)
+  end
+
+  doc.blocks = walk_blocks(doc.blocks)
+  return doc
 end
 
 return {
   set_wrapper = set_wrapper,
   filters = {
     { Pandoc = Pandoc },
-    { Code = Code },
+    { Pandoc = process_inline_code },
   },
 }

From e0b0f0c24752f54afe5258fcb42704e7a3719e0c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Micka=C3=ABl=20Canouil?=
 <8896044+mcanouil@users.noreply.github.com>
Date: Tue, 24 Mar 2026 17:21:44 +0100
Subject: [PATCH 2/8] fix: evaluate theorem title strings as Typst markup

Quarto renders custom type titles as title: "..." (string mode) which
stringifies any Typst markup. Inline code in titles produces Skylighting
tokens with inner quotes that break the Typst string syntax.

Two-part fix:
- Pre-quarto: convert Code in title scaffolds to plain Typst backtick
  code, avoiding Skylighting tokens that contain unescaped quotes.
- Post-quarto: inject a Typst override of simple-theorem-render that
  evaluates string titles with eval(mode: "markup"), giving title: [...]
  semantics even though Quarto emits title: "...".
---
 CHANGELOG.md                                  |  2 +-
 _extensions/code-window/_extension.yml        |  1 +
 .../_modules/hotfix/skylighting-typst-fix.lua | 26 +++---
 .../_modules/hotfix/typst-title-fix.lua       | 79 +++++++++++++++++++
 4 files changed, 91 insertions(+), 17 deletions(-)
 create mode 100644 _extensions/code-window/_modules/hotfix/typst-title-fix.lua

diff --git a/CHANGELOG.md b/CHANGELOG.md
index f0e3fd6..145c624 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,7 +5,7 @@
 ### Bug Fixes
 
 - fix: unwrap Quarto's `DecoratedCodeBlock` Div to prevent double filename wrapping in Typst output.
-- fix: prevent inline code in theorem/example titles from being converted to raw Typst markup that gets stringified.
+- fix: evaluate theorem/example title strings as Typst markup so inline code renders correctly instead of being stringified.
 - fix: normalise code blocks with no or unknown language class to `default` for consistent styling across all formats.
 - fix: default to `#` comment symbol for unknown code block languages (`default`, `txt`, etc.) in annotation detection.
 - fix: support code annotations with `syntax-highlighting: idiomatic` (native Typst highlighting) via a `show raw.line` rule.
diff --git a/_extensions/code-window/_extension.yml b/_extensions/code-window/_extension.yml
index 8badc0f..82af68a 100644
--- a/_extensions/code-window/_extension.yml
+++ b/_extensions/code-window/_extension.yml
@@ -6,3 +6,4 @@ contributes:
   filters:
     - at: pre-quarto
       path: main.lua
+    - path: _modules/hotfix/typst-title-fix.lua
diff --git a/_extensions/code-window/_modules/hotfix/skylighting-typst-fix.lua b/_extensions/code-window/_modules/hotfix/skylighting-typst-fix.lua
index 251766e..a409963 100644
--- a/_extensions/code-window/_modules/hotfix/skylighting-typst-fix.lua
+++ b/_extensions/code-window/_modules/hotfix/skylighting-typst-fix.lua
@@ -219,10 +219,6 @@ function Pandoc(doc)
 end
 
 --- Check if a Div is a Quarto title scaffold (inline-only content).
---- Quarto wraps theorem/example titles in __quarto_custom_scaffold Divs
---- containing a single Plain or Para block. Converting Code to RawInline
---- inside these Divs causes the raw Typst markup to be stringified as
---- literal text in the title parameter.
 --- @param div pandoc.Div
 --- @return boolean
 local function is_title_scaffold(div)
@@ -237,25 +233,23 @@ local function is_title_scaffold(div)
   return true
 end
 
---- Convert Code to plain Typst backtick code inside title scaffolds.
---- Prevents both the code-window box wrapping AND Pandoc's Skylighting
---- from generating Typst function calls that get stringified by Quarto.
---- @param el pandoc.Code
---- @return pandoc.RawInline
-local function neutralise_title_code(el)
-  return pandoc.RawInline('typst', '`' .. el.text .. '`')
-end
-
 --- Walk the document tree and convert inline Code to RawInline with
---- background styling, skipping title scaffolds where the conversion
---- would produce raw Typst markup that gets stringified by Quarto.
+--- background styling. Code in title scaffolds is converted to plain
+--- Typst backtick code to avoid Skylighting tokens with inner quotes
+--- that would break the string parameter Quarto generates.
+--- The typst-title-fix post-quarto filter then evaluates the string
+--- as markup so the backtick code renders with proper inline styling.
 local function process_inline_code(doc)
   if not quarto.doc.is_format('typst') then
     return doc
   end
 
   local code_filter = { Code = function(el) return process_typst_inline(el) end }
-  local title_filter = { Code = neutralise_title_code }
+  local title_filter = {
+    Code = function(el)
+      return pandoc.RawInline('typst', '`' .. el.text .. '`')
+    end,
+  }
 
   local function walk_blocks(blocks)
     local new_blocks = {}
diff --git a/_extensions/code-window/_modules/hotfix/typst-title-fix.lua b/_extensions/code-window/_modules/hotfix/typst-title-fix.lua
new file mode 100644
index 0000000..2da5040
--- /dev/null
+++ b/_extensions/code-window/_modules/hotfix/typst-title-fix.lua
@@ -0,0 +1,79 @@
+--- @module typst-title-fix
+--- @license MIT
+--- @copyright 2026 Mickaël Canouil
+--- @author Mickaël Canouil
+--- @brief Hot-fix for Quarto rendering theorem titles as string parameters.
+--- Quarto renders custom type titles as title: "..." (string mode) which
+--- stringifies any Typst markup. This filter injects a Typst show rule
+--- that evaluates string titles as markup so inline code and other
+--- formatting render correctly in theorem/example titles.
+
+--- Typst code that overrides simple-theorem-render to evaluate string
+--- titles as Typst markup. Injected after the template definitions so
+--- the override replaces the default. The make-frame calls are then
+--- re-created with the fixed render function.
+local TYPST_TITLE_FIX = [==[
+// code-window: hot-fix for Quarto rendering theorem titles as strings.
+// Redefine simple-theorem-render to evaluate string titles as Typst markup.
+// This produces title: [...] semantics even though Quarto emits title: "...".
+#let simple-theorem-render(prefix: none, title: "", full-title: auto, body) = {
+  if full-title != "" and full-title != auto and full-title != none {
+    let rendered-title = if type(full-title) == str {
+      eval(full-title, mode: "markup")
+    } else {
+      full-title
+    }
+    strong[#rendered-title.]
+    h(0.5em)
+  }
+  emph(body)
+  parbreak()
+}
+]==]
+
+return {
+  {
+    Pandoc = function(doc)
+      if not quarto.doc.is_format('typst') then
+        return doc
+      end
+
+      -- Only inject if there are __quarto_custom Theorem Divs in the document.
+      local has_theorems = false
+      local function check_blocks(blocks)
+        for _, blk in ipairs(blocks) do
+          if blk.t == 'Div' and blk.attributes['__quarto_custom_type'] == 'Theorem' then
+            has_theorems = true
+            return
+          end
+          if blk.t == 'Div' then
+            check_blocks(blk.content)
+          end
+        end
+      end
+      check_blocks(doc.blocks)
+      if not has_theorems then
+        return doc
+      end
+
+      -- Guard: skip if already injected.
+      for _, blk in ipairs(doc.blocks) do
+        if blk.t == 'RawBlock' and blk.format == 'typst'
+            and blk.text:find('code-window: hot-fix for Quarto rendering theorem titles', 1, true) then
+          return doc
+        end
+      end
+
+      -- Insert at the end of the preamble (before the first non-RawBlock).
+      local insert_pos = 1
+      for idx, blk in ipairs(doc.blocks) do
+        if blk.t ~= 'RawBlock' then
+          insert_pos = idx
+          break
+        end
+      end
+      table.insert(doc.blocks, insert_pos, pandoc.RawBlock('typst', TYPST_TITLE_FIX))
+      return doc
+    end,
+  },
+}

From 3321bcd8ca1f6fae31c7bc23fdeee93813c6a528 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Micka=C3=ABl=20Canouil?=
 <8896044+mcanouil@users.noreply.github.com>
Date: Tue, 24 Mar 2026 17:30:21 +0100
Subject: [PATCH 3/8] fix: wrap theorem functions to evaluate string titles as
 markup

The previous approach redefined simple-theorem-render, but make-frame
captures the render function by value at definition time, so the
override had no effect.

Instead, scan the Typst preamble for make-frame definitions, extract
the generated function names (e.g., example, theorem), and inject
wrapper functions that evaluate string title parameters with
eval(mode: "markup") before delegating to the original function.
---
 _extensions/code-window/_extension.yml        |  3 +-
 .../_modules/hotfix/typst-title-fix.lua       | 70 ++++++++++++-------
 2 files changed, 45 insertions(+), 28 deletions(-)

diff --git a/_extensions/code-window/_extension.yml b/_extensions/code-window/_extension.yml
index 82af68a..36c17df 100644
--- a/_extensions/code-window/_extension.yml
+++ b/_extensions/code-window/_extension.yml
@@ -6,4 +6,5 @@ contributes:
   filters:
     - at: pre-quarto
       path: main.lua
-    - path: _modules/hotfix/typst-title-fix.lua
+    - at: post-quarto
+      path: _modules/hotfix/typst-title-fix.lua
diff --git a/_extensions/code-window/_modules/hotfix/typst-title-fix.lua b/_extensions/code-window/_modules/hotfix/typst-title-fix.lua
index 2da5040..e7e0b5c 100644
--- a/_extensions/code-window/_modules/hotfix/typst-title-fix.lua
+++ b/_extensions/code-window/_modules/hotfix/typst-title-fix.lua
@@ -4,33 +4,34 @@
 --- @author Mickaël Canouil
 --- @brief Hot-fix for Quarto rendering theorem titles as string parameters.
 --- Quarto renders custom type titles as title: "..." (string mode) which
---- stringifies any Typst markup. This filter injects a Typst show rule
---- that evaluates string titles as markup so inline code and other
---- formatting render correctly in theorem/example titles.
+--- stringifies any Typst markup. This post-quarto filter scans the Typst
+--- preamble for make-frame definitions, then injects wrapper functions that
+--- evaluate string titles as Typst markup via eval(mode: "markup").
 
---- Typst code that overrides simple-theorem-render to evaluate string
---- titles as Typst markup. Injected after the template definitions so
---- the override replaces the default. The make-frame calls are then
---- re-created with the fixed render function.
-local TYPST_TITLE_FIX = [==[
-// code-window: hot-fix for Quarto rendering theorem titles as strings.
-// Redefine simple-theorem-render to evaluate string titles as Typst markup.
-// This produces title: [...] semantics even though Quarto emits title: "...".
-#let simple-theorem-render(prefix: none, title: "", full-title: auto, body) = {
-  if full-title != "" and full-title != auto and full-title != none {
-    let rendered-title = if type(full-title) == str {
-      eval(full-title, mode: "markup")
-    } else {
-      full-title
-    }
-    strong[#rendered-title.]
-    h(0.5em)
+--- Typst wrapper template. %s is replaced with the function name.
+local WRAPPER_TEMPLATE = [==[
+#let _cw-orig-%s = %s
+#let %s(title: none, ..args) = {
+  let t = if title != none and type(title) == str {
+    eval(title, mode: "markup")
+  } else {
+    title
   }
-  emph(body)
-  parbreak()
+  _cw-orig-%s(title: t, ..args)
 }
 ]==]
 
+--- Build Typst code that wraps each theorem function to eval string titles.
+--- @param func_names table List of function names to wrap
+--- @return string Typst code
+local function build_wrappers(func_names)
+  local parts = { '// code-window: hot-fix for Quarto rendering theorem titles as strings.' }
+  for _, name in ipairs(func_names) do
+    table.insert(parts, string.format(WRAPPER_TEMPLATE, name, name, name, name))
+  end
+  return table.concat(parts, '\n')
+end
+
 return {
   {
     Pandoc = function(doc)
@@ -64,15 +65,30 @@ return {
         end
       end
 
-      -- Insert at the end of the preamble (before the first non-RawBlock).
+      -- Scan preamble RawBlocks for make-frame definitions to find function names.
+      -- Pattern: #let (xxx-counter, xxx-box, xxx, show-xxx) = make-frame(
+      local func_names = {}
+      for _, blk in ipairs(doc.blocks) do
+        if blk.t == 'RawBlock' and blk.format == 'typst' then
+          for name in blk.text:gmatch('#let %([%w%-]+%-counter, [%w%-]+%-box, ([%w%-]+), show%-[%w%-]+%) = make%-frame%(') do
+            table.insert(func_names, name)
+          end
+        end
+      end
+
+      if #func_names == 0 then
+        return doc
+      end
+
+      -- Insert wrappers after the last make-frame definition.
       local insert_pos = 1
       for idx, blk in ipairs(doc.blocks) do
-        if blk.t ~= 'RawBlock' then
-          insert_pos = idx
-          break
+        if blk.t == 'RawBlock' and blk.format == 'typst'
+            and blk.text:find('make%-frame%(') then
+          insert_pos = idx + 1
         end
       end
-      table.insert(doc.blocks, insert_pos, pandoc.RawBlock('typst', TYPST_TITLE_FIX))
+      table.insert(doc.blocks, insert_pos, pandoc.RawBlock('typst', build_wrappers(func_names)))
       return doc
     end,
   },

From 6275453551d77442ccb8bbc586e74ce50108bec4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Micka=C3=ABl=20Canouil?=
 <8896044+mcanouil@users.noreply.github.com>
Date: Tue, 24 Mar 2026 17:37:05 +0100
Subject: [PATCH 4/8] fix: inject theorem wrappers via doc.blocks instead of
 header-includes

header-includes is placed before template definitions in the Typst
preamble, so the theorem functions are not yet defined. RawBlocks
inserted into doc.blocks appear after the template preamble, where
make-frame has already created the theorem functions.

Also scan the source file for cross-reference div IDs (e.g., #exm-,
#thm-) to determine which theorem functions to wrap, since this
information is not available in the AST at filter time.
---
 .../_modules/hotfix/typst-title-fix.lua       | 86 ++++++++++---------
 1 file changed, 44 insertions(+), 42 deletions(-)

diff --git a/_extensions/code-window/_modules/hotfix/typst-title-fix.lua b/_extensions/code-window/_modules/hotfix/typst-title-fix.lua
index e7e0b5c..02d67ef 100644
--- a/_extensions/code-window/_modules/hotfix/typst-title-fix.lua
+++ b/_extensions/code-window/_modules/hotfix/typst-title-fix.lua
@@ -4,10 +4,23 @@
 --- @author Mickaël Canouil
 --- @brief Hot-fix for Quarto rendering theorem titles as string parameters.
 --- Quarto renders custom type titles as title: "..." (string mode) which
---- stringifies any Typst markup. This post-quarto filter scans the Typst
---- preamble for make-frame definitions, then injects wrapper functions that
+--- stringifies any Typst markup. This post-quarto filter scans the source
+--- for cross-reference div IDs, then injects Typst wrapper functions that
 --- evaluate string titles as Typst markup via eval(mode: "markup").
 
+--- Mapping from Quarto cross-reference prefix to Typst function name.
+local PREFIX_TO_FUNC = {
+  thm = 'theorem',
+  lem = 'lemma',
+  cor = 'corollary',
+  prp = 'proposition',
+  cnj = 'conjecture',
+  def = 'definition',
+  exm = 'example',
+  exr = 'exercise',
+  sol = 'solution',
+}
+
 --- Typst wrapper template. %s is replaced with the function name.
 local WRAPPER_TEMPLATE = [==[
 #let _cw-orig-%s = %s
@@ -18,8 +31,7 @@ local WRAPPER_TEMPLATE = [==[
     title
   }
   _cw-orig-%s(title: t, ..args)
-}
-]==]
+}]==]
 
 --- Build Typst code that wraps each theorem function to eval string titles.
 --- @param func_names table List of function names to wrap
@@ -32,6 +44,28 @@ local function build_wrappers(func_names)
   return table.concat(parts, '\n')
 end
 
+--- Scan source files for cross-reference div IDs and return the
+--- corresponding Typst function names.
+--- @return table List of function names
+local function detect_theorem_types()
+  local func_names = {}
+  local seen = {}
+  for _, input_file in ipairs(PANDOC_STATE.input_files) do
+    local f = io.open(input_file, 'r')
+    if f then
+      local source = f:read('*a')
+      f:close()
+      for prefix in source:gmatch('::: *{#(%w+)%-') do
+        if PREFIX_TO_FUNC[prefix] and not seen[prefix] then
+          table.insert(func_names, PREFIX_TO_FUNC[prefix])
+          seen[prefix] = true
+        end
+      end
+    end
+  end
+  return func_names
+end
+
 return {
   {
     Pandoc = function(doc)
@@ -39,24 +73,6 @@ return {
         return doc
       end
 
-      -- Only inject if there are __quarto_custom Theorem Divs in the document.
-      local has_theorems = false
-      local function check_blocks(blocks)
-        for _, blk in ipairs(blocks) do
-          if blk.t == 'Div' and blk.attributes['__quarto_custom_type'] == 'Theorem' then
-            has_theorems = true
-            return
-          end
-          if blk.t == 'Div' then
-            check_blocks(blk.content)
-          end
-        end
-      end
-      check_blocks(doc.blocks)
-      if not has_theorems then
-        return doc
-      end
-
       -- Guard: skip if already injected.
       for _, blk in ipairs(doc.blocks) do
         if blk.t == 'RawBlock' and blk.format == 'typst'
@@ -65,30 +81,16 @@ return {
         end
       end
 
-      -- Scan preamble RawBlocks for make-frame definitions to find function names.
-      -- Pattern: #let (xxx-counter, xxx-box, xxx, show-xxx) = make-frame(
-      local func_names = {}
-      for _, blk in ipairs(doc.blocks) do
-        if blk.t == 'RawBlock' and blk.format == 'typst' then
-          for name in blk.text:gmatch('#let %([%w%-]+%-counter, [%w%-]+%-box, ([%w%-]+), show%-[%w%-]+%) = make%-frame%(') do
-            table.insert(func_names, name)
-          end
-        end
-      end
-
+      local func_names = detect_theorem_types()
       if #func_names == 0 then
         return doc
       end
 
-      -- Insert wrappers after the last make-frame definition.
-      local insert_pos = 1
-      for idx, blk in ipairs(doc.blocks) do
-        if blk.t == 'RawBlock' and blk.format == 'typst'
-            and blk.text:find('make%-frame%(') then
-          insert_pos = idx + 1
-        end
-      end
-      table.insert(doc.blocks, insert_pos, pandoc.RawBlock('typst', build_wrappers(func_names)))
+      -- Insert at the start of doc.blocks. RawBlocks placed here appear
+      -- after the Typst template preamble (where make-frame defines the
+      -- theorem functions), so the wrappers can reference them.
+      table.insert(doc.blocks, 1, pandoc.RawBlock('typst', build_wrappers(func_names)))
+
       return doc
     end,
   },

From 5b007b20080872e26eba989675191b9f272d5d61 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Micka=C3=ABl=20Canouil?=
 <8896044+mcanouil@users.noreply.github.com>
Date: Tue, 24 Mar 2026 23:00:40 +0100
Subject: [PATCH 5/8] feat: support per-hotfix quarto-version thresholds

Each hotfix can now have its own quarto-version threshold for
auto-disable, since upstream fixes are unlikely to land in the same
Quarto release. The hotfix value can be a boolean or a map with
enabled and quarto-version keys:

  hotfix:
    code-annotations:
      quarto-version: "1.10.0"
    skylighting:
      quarto-version: "1.11.0"
    typst-title:
      quarto-version: "1.10.0"

The global quarto-version key is still supported as a fallback.
Add typst-title as a new hotfix key for the theorem title fix.
---
 CHANGELOG.md                                  |  4 ++
 .../_modules/hotfix/typst-title-fix.lua       |  9 ++++
 _extensions/code-window/code-window.lua       | 46 ++++++++++++++++---
 3 files changed, 53 insertions(+), 6 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 145c624..e2dec39 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,10 @@
 - fix: default to `#` comment symbol for unknown code block languages (`default`, `txt`, etc.) in annotation detection.
 - fix: support code annotations with `syntax-highlighting: idiomatic` (native Typst highlighting) via a `show raw.line` rule.
 
+### New Features
+
+- feat: support per-hotfix `quarto-version` thresholds for independent auto-disable.
+
 ### Refactoring
 
 - refactor: extract language normalisation into dedicated `_modules/language.lua` module.
diff --git a/_extensions/code-window/_modules/hotfix/typst-title-fix.lua b/_extensions/code-window/_modules/hotfix/typst-title-fix.lua
index 02d67ef..7847f96 100644
--- a/_extensions/code-window/_modules/hotfix/typst-title-fix.lua
+++ b/_extensions/code-window/_modules/hotfix/typst-title-fix.lua
@@ -73,6 +73,15 @@ return {
         return doc
       end
 
+      -- Check if the hotfix is enabled via metadata set by the pre-quarto filter.
+      local hotfix_meta = doc.meta['_code-window-hotfix']
+      if hotfix_meta then
+        local enabled = hotfix_meta['typst-title']
+        if enabled and pandoc.utils.stringify(enabled) == 'false' then
+          return doc
+        end
+      end
+
       -- Guard: skip if already injected.
       for _, blk in ipairs(doc.blocks) do
         if blk.t == 'RawBlock' and blk.format == 'typst'
diff --git a/_extensions/code-window/code-window.lua b/_extensions/code-window/code-window.lua
index efd0ef3..3a7f9d5 100644
--- a/_extensions/code-window/code-window.lua
+++ b/_extensions/code-window/code-window.lua
@@ -43,6 +43,7 @@ local DEFAULTS = {
 local HOTFIX_DEFAULTS = {
   ['code-annotations'] = true,
   ['skylighting'] = true,
+  ['typst-title'] = true,
 }
 
 local CURRENT_FORMAT = nil
@@ -454,9 +455,13 @@ function Meta(meta)
       '"skylighting-fix" is deprecated. Use "hotfix: { skylighting: true/false }" instead.')
   end
 
-  -- Parse hotfix options with version-based auto-disable.
+  -- Parse hotfix options with per-hotfix version-based auto-disable.
+  -- Each hotfix value can be:
+  --   boolean/string: true/false to enable/disable
+  --   map: { enabled: true/false, quarto-version: "x.y.z" }
+  -- A global quarto-version key is also supported as a fallback.
   local hotfix = {}
-  local hotfix_version_override = false
+  local global_version_disabled = false
   if hotfix_meta then
     local version_str = hotfix_meta['quarto-version']
     if version_str then
@@ -464,17 +469,36 @@ function Meta(meta)
       if version_str ~= '' then
         local ok, threshold = pcall(pandoc.types.Version, version_str)
         if ok and quarto.version >= threshold then
-          hotfix_version_override = true
+          global_version_disabled = true
         end
       end
     end
   end
 
   for key, default in pairs(HOTFIX_DEFAULTS) do
-    if hotfix_version_override then
+    local entry = hotfix_meta and hotfix_meta[key]
+    if entry ~= nil and pandoc.utils.type(entry) == 'table' then
+      -- Map form: { enabled: bool, quarto-version: "x.y.z" }
+      local enabled = true
+      if entry['enabled'] ~= nil then
+        enabled = pandoc.utils.stringify(entry['enabled']) == 'true'
+      end
+      local ver = entry['quarto-version']
+      if ver then
+        ver = pandoc.utils.stringify(ver)
+        if ver ~= '' then
+          local ok, threshold = pcall(pandoc.types.Version, ver)
+          if ok and quarto.version >= threshold then
+            enabled = false
+          end
+        end
+      end
+      hotfix[key] = enabled
+    elseif entry ~= nil then
+      -- Simple boolean/string form
+      hotfix[key] = pandoc.utils.stringify(entry) == 'true'
+    elseif global_version_disabled then
       hotfix[key] = false
-    elseif hotfix_meta and hotfix_meta[key] ~= nil then
-      hotfix[key] = pandoc.utils.stringify(hotfix_meta[key]) == 'true'
     else
       hotfix[key] = default
     end
@@ -487,9 +511,19 @@ function Meta(meta)
     typst_wrapper = opts['wrapper'],
     hotfix_code_annotations = hotfix['code-annotations'],
     hotfix_skylighting = hotfix['skylighting'],
+    hotfix_typst_title = hotfix['typst-title'],
     code_annotations = annotations_enabled,
   }
 
+  -- Store hotfix state in metadata so the post-quarto typst-title-fix filter
+  -- can read it (it runs as a separate filter and has no access to CONFIG).
+  if not meta['_code-window-hotfix'] then
+    meta['_code-window-hotfix'] = {}
+  end
+  meta['_code-window-hotfix']['typst-title'] = pandoc.MetaString(
+    hotfix['typst-title'] and 'true' or 'false'
+  )
+
   -- Cache syntax highlighting background colour for Typst contrast-aware annotations.
   if CURRENT_FORMAT == 'typst' then
     local hm = PANDOC_WRITER_OPTIONS and PANDOC_WRITER_OPTIONS.highlight_method

From 26830683bb10f187efd2e80321a4c37c0a7357e3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Micka=C3=ABl=20Canouil?=
 <8896044+mcanouil@users.noreply.github.com>
Date: Sun, 29 Mar 2026 16:22:16 +0200
Subject: [PATCH 6/8] docs: drop global hotfix quarto-version and update
 schema/docs

Remove the global hotfix.quarto-version fallback in favour of per-hotfix
thresholds only. Update _schema.yml to use type: [boolean, object] instead
of anyOf (unsupported by quarto-wizard schema). Document the new
typst-title hotfix and per-hotfix map form in README. Add fragility
comments for internal Quarto dependencies.
---
 CHANGELOG.md                                  |  2 +-
 README.md                                     | 41 ++++++++++++++-----
 .../_modules/hotfix/skylighting-typst-fix.lua |  2 +
 .../_modules/hotfix/typst-title-fix.lua       |  4 ++
 _extensions/code-window/_schema.yml           | 36 ++++++++++++----
 _extensions/code-window/code-window.lua       | 17 --------
 6 files changed, 66 insertions(+), 36 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index e2dec39..6293c30 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -12,7 +12,7 @@
 
 ### New Features
 
-- feat: support per-hotfix `quarto-version` thresholds for independent auto-disable.
+- feat: replace global `hotfix.quarto-version` with per-hotfix thresholds for independent auto-disable.
 
 ### Refactoring
 
diff --git a/README.md b/README.md
index b160fe8..a2c37a1 100644
--- a/README.md
+++ b/README.md
@@ -59,9 +59,9 @@ extensions:
     style: "macos"
     wrapper: "code-window"
     hotfix:
-      quarto-version: ~
       code-annotations: true
       skylighting: true
+      typst-title: true
 ```
 
 ### Options
@@ -77,11 +77,13 @@ extensions:
 
 These options are **temporary** and will be removed in a future version (see [Temporary hot-fixes](#temporary-hot-fixes-typst)).
 
-| Option                    | Type    | Default | Description                                                                                |
-| ------------------------- | ------- | ------- | ------------------------------------------------------------------------------------------ |
-| `hotfix.quarto-version`   | string  | _unset_ | Quarto version at or above which all hot-fixes are automatically disabled.                 |
-| `hotfix.code-annotations` | boolean | `true`  | Enable the code-annotations hot-fix for Typst output.                                      |
-| `hotfix.skylighting`      | boolean | `true`  | Enable the Skylighting hot-fix for Typst output (overrides block styling and inline code). |
+Each hotfix value can be a simple boolean or a map with `enabled` and `quarto-version` keys for per-hotfix version thresholds.
+
+| Option                    | Type         | Default | Description                                                                                |
+| ------------------------- | ------------ | ------- | ------------------------------------------------------------------------------------------ |
+| `hotfix.code-annotations` | boolean/map  | `true`  | Enable the code-annotations hot-fix for Typst output.                                      |
+| `hotfix.skylighting`      | boolean/map  | `true`  | Enable the Skylighting hot-fix for Typst output (overrides block styling and inline code). |
+| `hotfix.typst-title`      | boolean/map  | `true`  | Enable the Typst title hot-fix (evaluates theorem title strings as markup).                |
 
 ### Styles
 
@@ -101,21 +103,37 @@ print("Windows style for this block only")
 
 ### Temporary Hot-fixes (Typst)
 
-The extension includes two temporary hot-fixes for Typst output that compensate for missing Quarto/Pandoc features.
-Both will be removed once [quarto-dev/quarto-cli#14170](https://github.com/quarto-dev/quarto-cli/pull/14170) is released.
+The extension includes three temporary hot-fixes for Typst output that compensate for missing Quarto/Pandoc features.
+All three will be removed once [quarto-dev/quarto-cli#14170](https://github.com/quarto-dev/quarto-cli/pull/14170) is released.
 After that, the extension will focus solely on **auto-filename** and **code-window-style** features.
 
 - **`hotfix.code-annotations`**: processes code annotation markers for Typst, since Quarto does not yet support `code-annotations` in Typst output.
   The `filename` attribute for code blocks will also become natively supported.
 - **`hotfix.skylighting`**: overrides Pandoc's Skylighting output for Typst to fix block and inline code styling.
+- **`hotfix.typst-title`**: evaluates theorem title strings as Typst markup so that inline formatting (e.g., code) renders correctly.
+
+Each hotfix can specify its own `quarto-version` threshold, since upstream fixes may land in different Quarto releases:
+
+```yaml
+extensions:
+  code-window:
+    hotfix:
+      code-annotations:
+        quarto-version: "1.10.0"
+      skylighting:
+        quarto-version: "1.11.0"
+      typst-title:
+        quarto-version: "1.10.0"
+```
 
-Set `hotfix.quarto-version` to automatically disable both hot-fixes once you update Quarto to the version that includes native support:
+The map form also accepts an `enabled` key to explicitly enable or disable a hotfix regardless of version:
 
 ```yaml
 extensions:
   code-window:
     hotfix:
-      quarto-version: "1.10.0"
+      skylighting:
+        enabled: false
 ```
 
 Future removal playbook:
@@ -124,7 +142,8 @@ Future removal playbook:
 2. Remove the `hotfix` section from `_schema.yml`.
 3. Remove the skylighting guard and loader in `main.lua`.
 4. Remove annotation processing from `code-window.lua`.
-5. Delete `_modules/hotfix/` directory entirely.
+5. Remove the typst-title fix filter and metadata bridge.
+6. Delete `_modules/hotfix/` directory entirely.
 
 ## Example
 
diff --git a/_extensions/code-window/_modules/hotfix/skylighting-typst-fix.lua b/_extensions/code-window/_modules/hotfix/skylighting-typst-fix.lua
index a409963..e872f0c 100644
--- a/_extensions/code-window/_modules/hotfix/skylighting-typst-fix.lua
+++ b/_extensions/code-window/_modules/hotfix/skylighting-typst-fix.lua
@@ -219,6 +219,8 @@ function Pandoc(doc)
 end
 
 --- Check if a Div is a Quarto title scaffold (inline-only content).
+--- NOTE: relies on Quarto's internal `__quarto_custom_scaffold` attribute,
+--- which is not part of the public API and may change without notice.
 --- @param div pandoc.Div
 --- @return boolean
 local function is_title_scaffold(div)
diff --git a/_extensions/code-window/_modules/hotfix/typst-title-fix.lua b/_extensions/code-window/_modules/hotfix/typst-title-fix.lua
index 7847f96..7f2361d 100644
--- a/_extensions/code-window/_modules/hotfix/typst-title-fix.lua
+++ b/_extensions/code-window/_modules/hotfix/typst-title-fix.lua
@@ -46,6 +46,8 @@ end
 
 --- Scan source files for cross-reference div IDs and return the
 --- corresponding Typst function names.
+--- NOTE: uses raw-text pattern matching on source files, so it will not
+--- detect divs inside `include` shortcodes or other indirect sources.
 --- @return table List of function names
 local function detect_theorem_types()
   local func_names = {}
@@ -98,6 +100,8 @@ return {
       -- Insert at the start of doc.blocks. RawBlocks placed here appear
       -- after the Typst template preamble (where make-frame defines the
       -- theorem functions), so the wrappers can reference them.
+      -- This relies on Quarto emitting the template preamble before
+      -- doc.blocks; if that ordering changes the wrappers will break.
       table.insert(doc.blocks, 1, pandoc.RawBlock('typst', build_wrappers(func_names)))
 
       return doc
diff --git a/_extensions/code-window/_schema.yml b/_extensions/code-window/_schema.yml
index 27a0c37..5ec2035 100644
--- a/_extensions/code-window/_schema.yml
+++ b/_extensions/code-window/_schema.yml
@@ -22,17 +22,39 @@ options:
     type: object
     description: "Temporary hot-fixes for Typst output. These will be removed when Quarto natively supports the corresponding features (see quarto-dev/quarto-cli#14170)."
     properties:
-      quarto-version:
-        type: string
-        description: "Quarto version at or above which all hot-fixes are automatically disabled. Leave unset to use individual toggles."
       code-annotations:
-        type: boolean
+        type: [boolean, object]
         default: true
-        description: "Enable the code-annotations hot-fix for Typst output."
+        description: "Enable the code-annotations hot-fix for Typst output. Use a boolean or a map with 'enabled' and 'quarto-version' keys."
+        properties:
+          enabled:
+            type: boolean
+            description: "Explicitly enable or disable this hot-fix."
+          quarto-version:
+            type: string
+            description: "Quarto version at or above which this hot-fix is automatically disabled."
       skylighting:
-        type: boolean
+        type: [boolean, object]
         default: true
-        description: "Enable the Skylighting hot-fix for Typst output (overrides block styling and adds inline code background)."
+        description: "Enable the Skylighting hot-fix for Typst output (overrides block styling and adds inline code background). Use a boolean or a map with 'enabled' and 'quarto-version' keys."
+        properties:
+          enabled:
+            type: boolean
+            description: "Explicitly enable or disable this hot-fix."
+          quarto-version:
+            type: string
+            description: "Quarto version at or above which this hot-fix is automatically disabled."
+      typst-title:
+        type: [boolean, object]
+        default: true
+        description: "Enable the Typst title hot-fix (evaluates theorem title strings as markup). Use a boolean or a map with 'enabled' and 'quarto-version' keys."
+        properties:
+          enabled:
+            type: boolean
+            description: "Explicitly enable or disable this hot-fix."
+          quarto-version:
+            type: string
+            description: "Quarto version at or above which this hot-fix is automatically disabled."
 
 attributes:
   CodeBlock:
diff --git a/_extensions/code-window/code-window.lua b/_extensions/code-window/code-window.lua
index 3a7f9d5..9ba139b 100644
--- a/_extensions/code-window/code-window.lua
+++ b/_extensions/code-window/code-window.lua
@@ -459,22 +459,7 @@ function Meta(meta)
   -- Each hotfix value can be:
   --   boolean/string: true/false to enable/disable
   --   map: { enabled: true/false, quarto-version: "x.y.z" }
-  -- A global quarto-version key is also supported as a fallback.
   local hotfix = {}
-  local global_version_disabled = false
-  if hotfix_meta then
-    local version_str = hotfix_meta['quarto-version']
-    if version_str then
-      version_str = pandoc.utils.stringify(version_str)
-      if version_str ~= '' then
-        local ok, threshold = pcall(pandoc.types.Version, version_str)
-        if ok and quarto.version >= threshold then
-          global_version_disabled = true
-        end
-      end
-    end
-  end
-
   for key, default in pairs(HOTFIX_DEFAULTS) do
     local entry = hotfix_meta and hotfix_meta[key]
     if entry ~= nil and pandoc.utils.type(entry) == 'table' then
@@ -497,8 +482,6 @@ function Meta(meta)
     elseif entry ~= nil then
       -- Simple boolean/string form
       hotfix[key] = pandoc.utils.stringify(entry) == 'true'
-    elseif global_version_disabled then
-      hotfix[key] = false
     else
       hotfix[key] = default
     end

From fd7a35cfa139ae3c1e510c4776a97b89e8213421 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Micka=C3=ABl=20Canouil?=
 <8896044+mcanouil@users.noreply.github.com>
Date: Sun, 29 Mar 2026 16:25:27 +0200
Subject: [PATCH 7/8] fix: use MetaMap for hotfix metadata bridge and guard
 file read

Use pandoc.MetaMap() instead of a plain Lua table when storing hotfix
state in document metadata, ensuring correct serialisation across filter
boundaries. Wrap f:read in pcall so the file handle is always closed
even if the read fails.
---
 _extensions/code-window/_modules/hotfix/typst-title-fix.lua | 3 ++-
 _extensions/code-window/code-window.lua                     | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/_extensions/code-window/_modules/hotfix/typst-title-fix.lua b/_extensions/code-window/_modules/hotfix/typst-title-fix.lua
index 7f2361d..3fd086c 100644
--- a/_extensions/code-window/_modules/hotfix/typst-title-fix.lua
+++ b/_extensions/code-window/_modules/hotfix/typst-title-fix.lua
@@ -55,8 +55,9 @@ local function detect_theorem_types()
   for _, input_file in ipairs(PANDOC_STATE.input_files) do
     local f = io.open(input_file, 'r')
     if f then
-      local source = f:read('*a')
+      local ok, source = pcall(f.read, f, '*a')
       f:close()
+      if not ok then source = '' end
       for prefix in source:gmatch('::: *{#(%w+)%-') do
         if PREFIX_TO_FUNC[prefix] and not seen[prefix] then
           table.insert(func_names, PREFIX_TO_FUNC[prefix])
diff --git a/_extensions/code-window/code-window.lua b/_extensions/code-window/code-window.lua
index 9ba139b..ce1d579 100644
--- a/_extensions/code-window/code-window.lua
+++ b/_extensions/code-window/code-window.lua
@@ -501,7 +501,7 @@ function Meta(meta)
   -- Store hotfix state in metadata so the post-quarto typst-title-fix filter
   -- can read it (it runs as a separate filter and has no access to CONFIG).
   if not meta['_code-window-hotfix'] then
-    meta['_code-window-hotfix'] = {}
+    meta['_code-window-hotfix'] = pandoc.MetaMap({})
   end
   meta['_code-window-hotfix']['typst-title'] = pandoc.MetaString(
     hotfix['typst-title'] and 'true' or 'false'

From ea9f61784c200649327eea5c83710a0b5dcf21f1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Micka=C3=ABl=20Canouil?=
 <8896044+mcanouil@users.noreply.github.com>
Date: Sun, 29 Mar 2026 16:29:24 +0200
Subject: [PATCH 8/8] fix: skip typst-title metadata bridge when extension is
 disabled

Guard the hotfix metadata bridge with CONFIG.enabled so the post-quarto
typst-title-fix filter does not inject wrappers when the extension is
turned off.
---
 _extensions/code-window/code-window.lua | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/_extensions/code-window/code-window.lua b/_extensions/code-window/code-window.lua
index ce1d579..d25047e 100644
--- a/_extensions/code-window/code-window.lua
+++ b/_extensions/code-window/code-window.lua
@@ -504,7 +504,7 @@ function Meta(meta)
     meta['_code-window-hotfix'] = pandoc.MetaMap({})
   end
   meta['_code-window-hotfix']['typst-title'] = pandoc.MetaString(
-    hotfix['typst-title'] and 'true' or 'false'
+    CONFIG.enabled and hotfix['typst-title'] and 'true' or 'false'
   )
 
   -- Cache syntax highlighting background colour for Typst contrast-aware annotations.