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LaTeX is pretty standard for typesetting math/CS texts of any length. You can use your favorite version control system, and write a Makefile to build a PDF/PS document.

If you want to make it easily readable on a webpage (and not just a PDF download), you may want to use html.

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I'll second latex it's really quite powerful and not that hard to use. Also if your on windows check out protex it's a bundle of everything you need to get started.

Also there are latex to html converters - I'm not too familiar with them.

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