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...but the error persisted...
What error?
To be clear, syntax highlighting of code blocks is NOT part of "standard" Markdown. If you get it added to the CommonMark specification, that is, by working with the CommonMark group and convincing them to make it a standard feature, once it's in the standard and implemented, it will just work in the Geany Markdown plugin. Until then, installing patches or extra packages won't help.
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