Well, I restarted Author Intrusion again. The last iteration was promising but I was spending my time working on reinventing stuff because I thought it was what I want. Earlier this week, I realized what it was and how I could use an existing library to hopefully avoid spinning wheels.
It does mean I can't use CSS selectors for phrases. Instead, I'll use XPath and C#'s XElement.
No `file.chapter word` and probably `//file[has-class('chapter')//word`.
Not as pretty but I need this working.
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I should have CWd that. Sorry.
I've always said that I'm writing AI for "programmers who are writers" so having a more complex query should be okay. If it saves me 30-50 hours not building up a CSS parse tree, then probably worth it. :)