Great article, thanks for sharing. Of relevance here is TiddlyWiki (www.tiddlywiki.com), a personal note taking tool, that includes some of the salient features, like transclusion and user-generated linking, mentioned in the article. In addition, the approach supports a built-in programming capability to allow computation on content (e.g., dynamic filtering and content generation) and extension via plugins. All information (content and Javascript code) is within a single html document.