diff --git a/tests/docs/smoke-all/issues/4820-giscus-dark-mode/darkly-default/.gitignore b/tests/docs/smoke-all/issues/4820-giscus-dark-mode/darkly-default/.gitignore
index 97ba89253e..4fd1d95257 100644
--- a/tests/docs/smoke-all/issues/4820-giscus-dark-mode/darkly-default/.gitignore
+++ b/tests/docs/smoke-all/issues/4820-giscus-dark-mode/darkly-default/.gitignore
@@ -1,2 +1,3 @@
 /.quarto/
-_site
\ No newline at end of file
+_site
+**/*.quarto_ipynb
diff --git a/tests/docs/smoke-all/issues/4820-giscus-dark-mode/darkly-default/_quarto.yml b/tests/docs/smoke-all/issues/4820-giscus-dark-mode/darkly-default/_quarto.yml
index 02722e01d0..37fc2888fc 100644
--- a/tests/docs/smoke-all/issues/4820-giscus-dark-mode/darkly-default/_quarto.yml
+++ b/tests/docs/smoke-all/issues/4820-giscus-dark-mode/darkly-default/_quarto.yml
@@ -4,7 +4,7 @@ project:
 website:
   comments:
     giscus:
-      repo: allenmanning/giscus-examples
+      repo: quarto-dev/quarto-cli
 
 format:
   html:
diff --git a/tests/docs/smoke-all/issues/4820-giscus-dark-mode/darkly-default/_index.qmd b/tests/docs/smoke-all/issues/4820-giscus-dark-mode/darkly-default/index.qmd
similarity index 100%
rename from tests/docs/smoke-all/issues/4820-giscus-dark-mode/darkly-default/_index.qmd
rename to tests/docs/smoke-all/issues/4820-giscus-dark-mode/darkly-default/index.qmd
diff --git a/tests/docs/smoke-all/issues/4820-giscus-dark-mode/darkly-light-cobalt/.gitignore b/tests/docs/smoke-all/issues/4820-giscus-dark-mode/darkly-light-cobalt/.gitignore
index 97ba89253e..4fd1d95257 100644
--- a/tests/docs/smoke-all/issues/4820-giscus-dark-mode/darkly-light-cobalt/.gitignore
+++ b/tests/docs/smoke-all/issues/4820-giscus-dark-mode/darkly-light-cobalt/.gitignore
@@ -1,2 +1,3 @@
 /.quarto/
-_site
\ No newline at end of file
+_site
+**/*.quarto_ipynb
diff --git a/tests/docs/smoke-all/issues/4820-giscus-dark-mode/darkly-light-cobalt/_quarto.yml b/tests/docs/smoke-all/issues/4820-giscus-dark-mode/darkly-light-cobalt/_quarto.yml
index b1b685c017..49cc85ccb3 100644
--- a/tests/docs/smoke-all/issues/4820-giscus-dark-mode/darkly-light-cobalt/_quarto.yml
+++ b/tests/docs/smoke-all/issues/4820-giscus-dark-mode/darkly-light-cobalt/_quarto.yml
@@ -4,7 +4,7 @@ project:
 website:
   comments:
     giscus:
-      repo: allenmanning/giscus-examples
+      repo: quarto-dev/quarto-cli
       theme:
         light: light
         dark: cobalt
diff --git a/tests/docs/smoke-all/issues/4820-giscus-dark-mode/darkly-light-cobalt/_index.qmd b/tests/docs/smoke-all/issues/4820-giscus-dark-mode/darkly-light-cobalt/index.qmd
similarity index 100%
rename from tests/docs/smoke-all/issues/4820-giscus-dark-mode/darkly-light-cobalt/_index.qmd
rename to tests/docs/smoke-all/issues/4820-giscus-dark-mode/darkly-light-cobalt/index.qmd
diff --git a/tests/docs/smoke-all/issues/4820-giscus-dark-mode/darkly-light-dark/.gitignore b/tests/docs/smoke-all/issues/4820-giscus-dark-mode/darkly-light-dark/.gitignore
index 97ba89253e..4fd1d95257 100644
--- a/tests/docs/smoke-all/issues/4820-giscus-dark-mode/darkly-light-dark/.gitignore
+++ b/tests/docs/smoke-all/issues/4820-giscus-dark-mode/darkly-light-dark/.gitignore
@@ -1,2 +1,3 @@
 /.quarto/
-_site
\ No newline at end of file
+_site
+**/*.quarto_ipynb
diff --git a/tests/docs/smoke-all/issues/4820-giscus-dark-mode/darkly-light-dark/_quarto.yml b/tests/docs/smoke-all/issues/4820-giscus-dark-mode/darkly-light-dark/_quarto.yml
index 935e435cad..b8d02ea694 100644
--- a/tests/docs/smoke-all/issues/4820-giscus-dark-mode/darkly-light-dark/_quarto.yml
+++ b/tests/docs/smoke-all/issues/4820-giscus-dark-mode/darkly-light-dark/_quarto.yml
@@ -4,7 +4,7 @@ project:
 website:
   comments:
     giscus:
-      repo: allenmanning/giscus-examples
+      repo: quarto-dev/quarto-cli
       theme:
         light: light
         dark: dark
diff --git a/tests/docs/smoke-all/issues/4820-giscus-dark-mode/darkly-light-dark/_index.qmd b/tests/docs/smoke-all/issues/4820-giscus-dark-mode/darkly-light-dark/index.qmd
similarity index 100%
rename from tests/docs/smoke-all/issues/4820-giscus-dark-mode/darkly-light-dark/_index.qmd
rename to tests/docs/smoke-all/issues/4820-giscus-dark-mode/darkly-light-dark/index.qmd
diff --git a/tests/docs/smoke-all/issues/4820-giscus-dark-mode/lightly-cobalt_only/.gitignore b/tests/docs/smoke-all/issues/4820-giscus-dark-mode/lightly-cobalt_only/.gitignore
index 97ba89253e..4fd1d95257 100644
--- a/tests/docs/smoke-all/issues/4820-giscus-dark-mode/lightly-cobalt_only/.gitignore
+++ b/tests/docs/smoke-all/issues/4820-giscus-dark-mode/lightly-cobalt_only/.gitignore
@@ -1,2 +1,3 @@
 /.quarto/
-_site
\ No newline at end of file
+_site
+**/*.quarto_ipynb
diff --git a/tests/docs/smoke-all/issues/4820-giscus-dark-mode/lightly-cobalt_only/_quarto.yml b/tests/docs/smoke-all/issues/4820-giscus-dark-mode/lightly-cobalt_only/_quarto.yml
index 8eecb4ff17..da279b3602 100644
--- a/tests/docs/smoke-all/issues/4820-giscus-dark-mode/lightly-cobalt_only/_quarto.yml
+++ b/tests/docs/smoke-all/issues/4820-giscus-dark-mode/lightly-cobalt_only/_quarto.yml
@@ -4,11 +4,11 @@ project:
 website:
   comments:
     giscus:
-      repo: allenmanning/giscus-examples
+      repo: quarto-dev/quarto-cli
       theme: cobalt
 
 format:
   html:
     theme:
       light: lightly
-      dark: darkly
\ No newline at end of file
+      dark: darkly
diff --git a/tests/docs/smoke-all/issues/4820-giscus-dark-mode/lightly-cobalt_only/_index.qmd b/tests/docs/smoke-all/issues/4820-giscus-dark-mode/lightly-cobalt_only/index.qmd
similarity index 100%
rename from tests/docs/smoke-all/issues/4820-giscus-dark-mode/lightly-cobalt_only/_index.qmd
rename to tests/docs/smoke-all/issues/4820-giscus-dark-mode/lightly-cobalt_only/index.qmd
diff --git a/tests/docs/smoke-all/issues/4820-giscus-dark-mode/lightly-default/.gitignore b/tests/docs/smoke-all/issues/4820-giscus-dark-mode/lightly-default/.gitignore
index 97ba89253e..4fd1d95257 100644
--- a/tests/docs/smoke-all/issues/4820-giscus-dark-mode/lightly-default/.gitignore
+++ b/tests/docs/smoke-all/issues/4820-giscus-dark-mode/lightly-default/.gitignore
@@ -1,2 +1,3 @@
 /.quarto/
-_site
\ No newline at end of file
+_site
+**/*.quarto_ipynb
diff --git a/tests/docs/smoke-all/issues/4820-giscus-dark-mode/lightly-default/_quarto.yml b/tests/docs/smoke-all/issues/4820-giscus-dark-mode/lightly-default/_quarto.yml
index 64a572e5d9..d3d21152fa 100644
--- a/tests/docs/smoke-all/issues/4820-giscus-dark-mode/lightly-default/_quarto.yml
+++ b/tests/docs/smoke-all/issues/4820-giscus-dark-mode/lightly-default/_quarto.yml
@@ -4,10 +4,10 @@ project:
 website:
   comments:
     giscus:
-      repo: allenmanning/giscus-examples
+      repo: quarto-dev/quarto-cli
 
 format:
   html:
     theme:
       light: lightly
-      dark: darkly
\ No newline at end of file
+      dark: darkly
diff --git a/tests/docs/smoke-all/issues/4820-giscus-dark-mode/lightly-default/_index.qmd b/tests/docs/smoke-all/issues/4820-giscus-dark-mode/lightly-default/index.qmd
similarity index 100%
rename from tests/docs/smoke-all/issues/4820-giscus-dark-mode/lightly-default/_index.qmd
rename to tests/docs/smoke-all/issues/4820-giscus-dark-mode/lightly-default/index.qmd
diff --git a/tests/docs/smoke-all/issues/4820-giscus-dark-mode/lightly-light-cobalt/.gitignore b/tests/docs/smoke-all/issues/4820-giscus-dark-mode/lightly-light-cobalt/.gitignore
index 97ba89253e..4fd1d95257 100644
--- a/tests/docs/smoke-all/issues/4820-giscus-dark-mode/lightly-light-cobalt/.gitignore
+++ b/tests/docs/smoke-all/issues/4820-giscus-dark-mode/lightly-light-cobalt/.gitignore
@@ -1,2 +1,3 @@
 /.quarto/
-_site
\ No newline at end of file
+_site
+**/*.quarto_ipynb
diff --git a/tests/docs/smoke-all/issues/4820-giscus-dark-mode/lightly-light-cobalt/_quarto.yml b/tests/docs/smoke-all/issues/4820-giscus-dark-mode/lightly-light-cobalt/_quarto.yml
index 76d4660aa6..f9743b1822 100644
--- a/tests/docs/smoke-all/issues/4820-giscus-dark-mode/lightly-light-cobalt/_quarto.yml
+++ b/tests/docs/smoke-all/issues/4820-giscus-dark-mode/lightly-light-cobalt/_quarto.yml
@@ -4,7 +4,7 @@ project:
 website:
   comments:
     giscus:
-      repo: allenmanning/giscus-examples
+      repo: quarto-dev/quarto-cli
       theme:
         light: light
         dark: cobalt
@@ -13,4 +13,4 @@ format:
   html:
     theme:
       light: lightly
-      dark: darkly
\ No newline at end of file
+      dark: darkly
diff --git a/tests/docs/smoke-all/issues/4820-giscus-dark-mode/lightly-light-cobalt/_index.qmd b/tests/docs/smoke-all/issues/4820-giscus-dark-mode/lightly-light-cobalt/index.qmd
similarity index 100%
rename from tests/docs/smoke-all/issues/4820-giscus-dark-mode/lightly-light-cobalt/_index.qmd
rename to tests/docs/smoke-all/issues/4820-giscus-dark-mode/lightly-light-cobalt/index.qmd