Fix configuration

Author: gaow

manuscript-website/_config.yml

@@ -22,3 +22,8 @@ html:
   use_issues_button: true
   use_repository_button: true
 
+# Add navigation depth configuration to show one level expanded by default
+sphinx:
+  config:
+    html_theme_options:
+      show_navbar_depth: 1

manuscript-website/_toc.yml

@@ -3,8 +3,6 @@
 
 format: jb-book
 root: index
-defaults:
-  expand_sections: true  # Make all sections expand by default
 chapters:
   - file: intro
   - file: Main_Figures/index