PDF is pretty much brain-dead. It’ll work in a very basic sense, but I certainly wouldn’t want to use that option if I could possibly help it.
As mentioned late on in that multi-year-spanning thread, you can use an app such as Goodreader to store your entire site folder on your iPad. The easiest way to get it into GoodReader is to zip the site folder to transfer then unzip it in the app afterwards. Browsing is done within GoodReader.
That’s the best traditional option, but there are other ways to go. I’m currently exploring CircularFLO, an EPUB-generating tool that works with InDesign but (thanks to its extremely cooperative and experiment-friendly developer) can now also embed any ‘self-contained’ HTML & resources within a fixed-layout (FXL) EPUB document. My primary reason, other than sheer curiosity, is to be able to put my interactive panoramic photography into ebooks, but it should work for all sorts of tasks as long as the HTML doesn’t try to make any references to anything external.
The workflow goes like this: make a regular page layout using Adobe InDesign (version CS6 or newer), use CircularFLO to add your custom HTML to the page and make any other ebook-specific additions, then export an EPUB using CircularFLO. InDesign’s own fixed-layout EPUB abilities are still pretty basic even in the current revision of CC.
This is pretty damn new stuff, but it’s technically valid. It works well and any decent FXL EPUB-compatible e-reader (iBooks, Adobe Digital Editions 4, Kobo, and others) will take it in its stride. See http://CircularFLO.com for info.
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