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If I do:

let &makeprg = 'pandoc --from=markdown --output %:p:r:S.$* -- %:p:S' 

Then:

:make html 

generate the command:

pandoc --from=markdown --output "myfolder/myfile".html -- "myfolder/myfile" 

Maybe you would like to do:

let &makeprg = 'pandoc --from=markdown --output "%:p:r.$*" -- %:p:S' 

that generates:

pandoc --from=markdown --output "myfolder/myfile.html" -- "myfolder/myfile"