I am guessing you want to create a HTML File with Title Page or Header Information. The solution is to do it in more than one Step.
First you compile the Title Page together any other pages to one html.
$ pandoc .1_HEADER.markdown -o header.html
Then you include that header.html before the body:
$ pandoc -s -S --toc -B .header.html .2_Document.markdown -o complete_doc.html
Done.
The pandoc help states it's possibilities to make multi-part documents possible, both -B and -H work, but i think -B is more correct in my case.
-H FILENAME --include-in-header=FILENAME
-B FILENAME --include-before-body=FILENAME
-A FILENAME --include-after-body=FILENAME
In my case i do it with a stylesheet and get a perfect document:
$ pandoc -s -S -c .
esgithub-pandoc.css .1_HEADER.markdown -o header.html
$ pandoc -s -S --toc --toc-depth=2 -c .
esgithub-pandoc.css -B .header.html .2_Document.markdown -o complete_document.html
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