add partial hunks from non-ast changes

Author: cscheid

package/src/common/prepare-dist.ts

@@ -143,9 +143,14 @@ function inlineFilters(config: Configuration) {
   info("Building inlined filters");
   const outDir = join(config.directoryInfo.share, "filters");
   const filtersToInline: Filter[] = [
-    { name: "main", dir: "." },
+    { name: "quarto-init" },
+    { name: "authors" },
+    { name: "quarto-pre" },
+    { name: "crossref" },
+    { name: "layout" },
+    { name: "quarto-post" },
     { name: "pagebreak", dir: "rmarkdown" },
-    { name: "customwriter", dir: "customwriter" },
+    { name: "quarto-finalize" },
   ];
 
   filtersToInline.forEach((filter) => {

src/command/render/pandoc.ts

@@ -722,6 +722,13 @@ export async function runPandoc(
     pandocArgs = removePandocArgs(pandocArgs, removeArgs);
   }
 
+  // https://github.com/quarto-dev/quarto-cli/issues/3126
+  // it seems that we still need to coerce number-offset to be an number list,
+  // otherwise pandoc fails.
+  if (typeof allDefaults[kNumberOffset] === "number") {
+    allDefaults[kNumberOffset] = [allDefaults[kNumberOffset]];
+  }
+
   // We always use our own pandoc data-dir, so tear off the user
   // data-dir and use ours.
   const dataDirArgs = new Map<string, boolean>();