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odamizu,
If you had an earlier version of Doitsu's Markdown plugin installed and its prefs are not empty, then it will assume it knows the path to the cmark executable and will not run os.chmod on the binary.
The easiest approach it to temporarily rename the Markdown preferences folder once. Then fire up Markdown and it will look for the new cmark executable and properly chmod it to be executable.
You should be able to put the renamed Markdown prefs folder back or just set new preferences.
This worked for me.
I will build a universal binary for macOS and provide it to Doitsu when I am home and have access to my arm64 machine.
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