Just to mention another disadvantage of -M option that I haven’t included 
in the summary above: if the options is specified in this way, it will 
“burn-into” the document. But one of the application I need is to go freely 
in a round trip (converting pandoc Table to CSV CodeBlock in one pass, and 
convert the CSV CodeBlock back to pandoc Table in another pass). But since 
the -M metadata will accumulate, this is a no-go at least for me. Because 
of this, I now see why @jgm recommends using environment variables among 
the currently working methods. But the potential difficulties for Windows 
users is still a concern.

And the new suggestions of -F FILTERNAME[=FILTEROPTIONS] seems cleanest. 
For ugly filter name: -F "My Cool Filter.py"="--some --cool --arg". Don’t 
know if this will make the life of pandoc-mode or panzer and alike easier 
too.
​

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