From f27ceae76c8222e953b7b4508d368d9fd11c539b Mon Sep 17 00:00:00 2001
From: Christophe Dervieux <christophe.dervieux@gmail.com>
Date: Fri, 4 Apr 2025 12:29:03 +0200
Subject: [PATCH 1/3] don't loose DOCTYPE header in embed resource processing

---
 src/core/pandoc/self-contained.ts                             | 4 ++++
 .../formats/html/pandoc-selfcontained/selfcontained.html      | 1 +
 2 files changed, 5 insertions(+)

diff --git a/src/core/pandoc/self-contained.ts b/src/core/pandoc/self-contained.ts
index ca3e9f55aee..58337886cb3 100644
--- a/src/core/pandoc/self-contained.ts
+++ b/src/core/pandoc/self-contained.ts
@@ -48,6 +48,7 @@ export const pandocIngestSelfContainedContent = async (
 
   // The raw html contents
   const contents = Deno.readTextFileSync(file);
+  const doctypeMatch = contents.match(/^<!DOCTYPE.*?>/);
   const dom = await parseHtml(contents);
   await bundleModules(dom, workingDir);
 
@@ -63,6 +64,9 @@ export const pandocIngestSelfContainedContent = async (
   cmd.push("--template", template);
   cmd.push("--output", filename);
   cmd.push("--metadata", "title=placeholder");
+  if (doctypeMatch) {
+    cmd.push("--variable", `doctype=${doctypeMatch[0]}`);
+  }
   cmd.push("--embed-resources");
   if (resourcePath && resourcePath.length) {
     cmd.push("--resource-path", resourcePath.join(":"));
diff --git a/src/resources/formats/html/pandoc-selfcontained/selfcontained.html b/src/resources/formats/html/pandoc-selfcontained/selfcontained.html
index f37d7c6dce5..b835db8363c 100644
--- a/src/resources/formats/html/pandoc-selfcontained/selfcontained.html
+++ b/src/resources/formats/html/pandoc-selfcontained/selfcontained.html
@@ -1 +1,2 @@
+$if(doctype)$$doctype$$endif$
 $body$
\ No newline at end of file

From 32550eea455fa9f899f98513f65ee88af27f3f69 Mon Sep 17 00:00:00 2001
From: Christophe Dervieux <christophe.dervieux@gmail.com>
Date: Fri, 4 Apr 2025 12:36:58 +0200
Subject: [PATCH 2/3] Add a regression test for DOCTYPE presence

---
 tests/docs/smoke-all/2025/04/04/12295.qmd | 28 +++++++++++++++++++++++
 1 file changed, 28 insertions(+)
 create mode 100644 tests/docs/smoke-all/2025/04/04/12295.qmd

diff --git a/tests/docs/smoke-all/2025/04/04/12295.qmd b/tests/docs/smoke-all/2025/04/04/12295.qmd
new file mode 100644
index 00000000000..13a9eff71dc
--- /dev/null
+++ b/tests/docs/smoke-all/2025/04/04/12295.qmd
@@ -0,0 +1,28 @@
+---
+title: DOCTYPE is not lost when using embed-resources
+embed-resources: true
+_quarto:
+  tests:
+    html:
+      ensureHtmlElements:
+        - []
+        - []
+      ensureFileRegexMatches:
+        - ['\<\!DOCTYPE html\>'] 
+        - []
+    revealjs:
+      ensureHtmlElements:
+        - []
+        - []
+      ensureFileRegexMatches:
+        - ['\<\!DOCTYPE html\>'] 
+        - []
+---
+
+Example from https://github.com/quarto-dev/quarto-cli/issues/12295: Not having DOCTYPE lead to browser using a Quirk mode for CSS, and not applying the standard HTML5. 
+
+## Header
+
+```bash
+quarto render --help
+```
\ No newline at end of file

From caae7f2d10897eb1769f3c781e53290f0a19e01b Mon Sep 17 00:00:00 2001
From: Christophe Dervieux <christophe.dervieux@gmail.com>
Date: Fri, 4 Apr 2025 12:56:31 +0200
Subject: [PATCH 3/3] don't use Pandoc variable to avoid problem for complex
 DOCTYPE

---
 src/core/pandoc/self-contained.ts                           | 6 +++---
 .../formats/html/pandoc-selfcontained/selfcontained.html    | 1 -
 2 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/src/core/pandoc/self-contained.ts b/src/core/pandoc/self-contained.ts
index 58337886cb3..252f7181466 100644
--- a/src/core/pandoc/self-contained.ts
+++ b/src/core/pandoc/self-contained.ts
@@ -54,6 +54,9 @@ export const pandocIngestSelfContainedContent = async (
 
   const input: string[] = [];
   input.push("````````{=html}");
+  if (doctypeMatch) {
+    input.push(doctypeMatch[0]);
+  }
   input.push(dom.documentElement!.outerHTML);
   input.push("````````");
 
@@ -64,9 +67,6 @@ export const pandocIngestSelfContainedContent = async (
   cmd.push("--template", template);
   cmd.push("--output", filename);
   cmd.push("--metadata", "title=placeholder");
-  if (doctypeMatch) {
-    cmd.push("--variable", `doctype=${doctypeMatch[0]}`);
-  }
   cmd.push("--embed-resources");
   if (resourcePath && resourcePath.length) {
     cmd.push("--resource-path", resourcePath.join(":"));
diff --git a/src/resources/formats/html/pandoc-selfcontained/selfcontained.html b/src/resources/formats/html/pandoc-selfcontained/selfcontained.html
index b835db8363c..f37d7c6dce5 100644
--- a/src/resources/formats/html/pandoc-selfcontained/selfcontained.html
+++ b/src/resources/formats/html/pandoc-selfcontained/selfcontained.html
@@ -1,2 +1 @@
-$if(doctype)$$doctype$$endif$
 $body$
\ No newline at end of file