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Anything specific I should try to get a web HTML doc into a nice ebook format?
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The word "nice" is subjective but I would suggest you flatten the web site to be read linearly as a book instead of a web site. Web sites are not designed to be books and are optimized to load pages quickly on Gramma's dial-up and consequently have quite an 'exploded' structre. To make it 'nice' will require some manual manipulation on your part.
So, on ideas to make it a "nice" ebook, I would think you need to take the site and flatten it manually so that instead of having an exploded structure it is linear like a normal book. If the html files are all sequentially numbered in the order you want them in, like pages in a book, you can easily stitch them together as one file and then add chapter markers and a TOC on the first page. Or, their filenames can be adjusted according to an index you create or modify and then possibly loaded into calibre by adding that index instead.
I would use textutil to concatenate smaller files into a large file for each chapter or the whole book depending on how large it is. Then import it into calibre or add it to your Kindle.
Textutil is a unix tool that is found on Linux and Mac OSX also. If you are using Windows I am sure there is some utility that does the same thing.
http://www.unix.com/man-page/All/1/TEXTUTIL/
http://oreilly.com/pub/a/mac/2005/11/22/cli-tools.html
Happy Wednesday
Archon