An EPUB 3.0 template to help you get started with your ebook. (Includes iBooks display options.)
http://git.io/epub3-boilerplate
▾ /
▾ META-INF/
▪ container.xml
▪ mimetype
▾ OPS/ (Open Publishing Structure)
▾ book/
▪ content.html
▪ cover.html
▪ title.html
▪ table-of-contents.html
▪ table-of-contents.ncx
▾ css/
▪ style.css
▾ fonts/
▪ fonts.css
▪ someawesomefont.woff
▾ images/
▪ cover.jpg
▪ package.opf
As the author of this template I myself have used it a lot already and everytime I find something new I need in a book, I add it to this template. So, what I suggest you do is you really start fresh, creating a new folder and adding only what you need, otherwise I find it tough to keep track of what you have changed, added or deleted. Have fun coding!