This is a setup I made myself to be able to quickly create a book with Markdown, to worry about layout etc later.
Simply edit the start and stop files to change the resulting book page, and startc and stopc to edit the html surrounding the chapters.
Create a list of files in order of the chapters in an index file (example available in exampleindex) and create the html with ./publish exampleindex.
As long as you use the correct path in the index-file, you can put your files in any configuration you want. And of course you can edit the publish-script to do even more wonderful things. Remember, this is just a basic setup for writing a book, it's not all you can get.