allow pandoc to handle section numbering for markdown formats

Author: jjallaire

src/command/render/pandoc.ts

@@ -43,6 +43,7 @@ import {
   isHtmlOutput,
   isIpynbOutput,
   isLatexOutput,
+  isMarkdownOutput,
 } from "../../config/format.ts";
 import {
   isIncludeMetadata,
@@ -636,7 +637,10 @@ export async function runPandoc(
   // remove selected args and defaults if we are handling some things on behalf of pandoc
   // (e.g. handling section numbering). note that section numbering is handled by the
   // crossref filter so we only do this if the user hasn't disabled the crossref filter
-  if (!isLatexOutput(options.format.pandoc) && crossrefFilterActive(options)) {
+  if (
+    !isLatexOutput(options.format.pandoc) &&
+    !isMarkdownOutput(options.format.pandoc) && crossrefFilterActive(options)
+  ) {
     delete allDefaults[kNumberSections];
     delete allDefaults[kNumberOffset];
     const removeArgs = new Map<string, boolean>();

src/resources/filters/crossref/sections.lua

@@ -61,10 +61,14 @@ function sections()
           el.content:insert(1, pandoc.Space())
         end
 
-        el.content:insert(1, pandoc.Span(
-          stringToInlines(section),
-          pandoc.Attr("", { "header-section-number"})
-        ))
+        if _quarto.format.isHtmlOutput() then
+          el.content:insert(1, pandoc.Span(
+            stringToInlines(section),
+            pandoc.Attr("", { "header-section-number"})
+          ))
+        else
+          tprepend(el.content, stringToInlines(section))
+        end
 
         if appendix then
           el.content:insert(1, pandoc.Space())
@@ -93,7 +97,9 @@ function currentSectionLevel()
 end
 
 function numberSections()
-  return not _quarto.format.isLatexOutput() and numberSectionsOptionEnabled()
+  return not _quarto.format.isLatexOutput() and 
+         not _quarto.format.isMarkdownOutput() 
+         and numberSectionsOptionEnabled()
 end
 
 function numberSectionsOptionEnabled()