One of the primary goals is for search engines to index content from the trilogy sites and provide high-ranking search results. Is there anything outside of general SEO practices that can be done within the confines of the trilogy UI to help improve search results? Or, in other words, are there ways to structure questions and answers such that meld with SEO practices? Any caveats to Markdown that could hurt rankings? Obviously using relevant keywords and descriptive phrasing so the index has more to go on, but what else can help or hurt the index rankings?
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The most influential action a user can take to encourage the search engines to link to your content to
Use a Clear, Well-Thought-Out Title.
The title of a question (which becomes part of URL) carries a significant weight when it comes to search engine rankings.
I'm not sure if you noticed this or not, but Google already handles the Trilogy pretty well. I can honestly say that almost any time I Google a programming question, the Trilogy is first page, and often top listing -- assuming said question was already asked here.
I suppose it's possible for us to screw up our Markdown so badly that we hurt a given question's indexing. For example, overuse of images and underuse of text would definitely cause some issues. But by the time the answers get in and indexed, even that will likely be low-impact.
I think it would be interesting to do a keyword analysis on top google searches where we would like to appear, and then incorporate such verbage in our questions and answers.