Pandoc is a great for converting text.
Markdown to HTML, to LaTeX, to PDF, etc.
Pandoc does process a lot of raw latex features while converting markdown to PDF, like:
Title
===
\tableofcontents
\pagebreak
# Hello World
* Line 1
* Line 2
BUT, pandoc can't process \includes. Pandoc can only concatenate documents in a row, so you can't do:
Title
===
\tableofcontents
\pagebreak
# Hello World
* Line 1
* Line 2
\include{chapter01.md}
So, I've created a simple preprocessor in python. It reads your files and process all includes in the document, generating a bigger document. It's recursive, so you can nest several includes.
Check out the code and how to use in github: https://github.com/george-silva/pandoc-preprocessor