diff --git a/include/CLI/Config.hpp b/include/CLI/Config.hpp
index 8dfcddd9..a91f0da6 100644
--- a/include/CLI/Config.hpp
+++ b/include/CLI/Config.hpp
@@ -14,7 +14,7 @@
 #include <string>
 #include <utility>
 #include <vector>
-// [CLI11:public_includes:set]
+// [CLI11:public_includes:end]
 
 #include "App.hpp"
 #include "ConfigFwd.hpp"
diff --git a/scripts/MakeSingleHeader.py b/scripts/MakeSingleHeader.py
index 4bc53dd1..7cca6f70 100755
--- a/scripts/MakeSingleHeader.py
+++ b/scripts/MakeSingleHeader.py
@@ -80,7 +80,7 @@ class HeaderGroups(dict):
         """
         for key in self:
             if isinstance(self[key], set):
-                self[key] = "\n".join(self[key])
+                self[key] = "\n".join(sorted(self[key]))
 
 
 def make_header(output, main_header, files, tag, namespace, macro=None, version=None):
@@ -100,6 +100,8 @@ def make_header(output, main_header, files, tag, namespace, macro=None, version=
         groups["git"] = ""
 
     for f in files:
+        if os.path.isdir(f):
+            continue
         groups.read_header(f)
 
     groups["namespace"] = namespace