This evening while I was reestablishing Kobashi Computing after a hacker attack rendered it useless, I went about configuring all my modules and settings. After doing a quick look at the site pages, I noticed some errors in rendering code fragments in my pages.
I immediately thought of the code filter module and that it was missing - yes it was. But after installing it, the code fragments were still rendering incorrectly in the articles.
It just so happens that I had the wrong input format ordering all along and they really need to be like this:

Now, I get the proper code fragments being parsed correctly by the code filter and looking cool.
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