The issue with the orphans plugin not taking inlining into account is documented in the plugin's page. I'm not sure of the value of checking for this, at least for blog-type things, since unless you set up archive pages, any blog post will eventually fall off the blog and be orphaned, even if it wasn't before. What I do is use something like pages="* and !*/blog" to exclude all pages in the blog.
Good point about CSS files, although of course ikiwiki can't even try to parse out literal <link rel=stylesheet> html. But it would be good if the orphans plugin was aware of [[meta link="foo.css" rel="stylesheet"]]. -- see shy jo
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