You can develop toc.xml files using the Table of Contents Editor provided by PDE and UA. To create a new table of contents, simply select File > New > Other... > User Assistance > Help Table of Contents and choose a project and file name for your table of contents.
As for the HTML files, you can write them by hand, which is painful. There are many alternatives, such as DocBook, for those who swear by XML, style sheets, and XSLT, or the HTML editor included as a sample with this book.