Fixed loops that were in the wrong order.

src/Literate.jl

@@ -552,7 +552,7 @@ function containsYAML(chunk)
         if startswith(strip(line.first * line.second), "!!! carp")
             return true
         end
-end
+    #???
     return false
 end
 
@@ -677,9 +677,10 @@ function markdown(inputfile, outputdir=pwd(); config::AbstractDict=Dict(), kwarg
     sb = sandbox()
     iomd = IOBuffer()
     
+    
+    if flavor isa CarpentriesFlavor
         for chunk in chunks
             io = IOBuffer()
-        if flavor isa CarpentriesFlavor
             if isa(chunk, MDChunk)
                 if containsAdmonition(chunk)
 
@@ -728,6 +729,7 @@ function markdown(inputfile, outputdir=pwd(); config::AbstractDict=Dict(), kwarg
                         )
                     end
             end
+        end
     else
         # Vanilla Function
         for (chunknum, chunk) in enumerate(chunks)
@@ -788,7 +790,7 @@ function markdown(inputfile, outputdir=pwd(); config::AbstractDict=Dict(), kwarg
         end
     end
         write(iomd, '\n') # add a newline between each chunk
-    end
+
 
     # custom post-processing from user
     content = config["postprocess"](String(take!(iomd)))