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@thisisthebreath @DaemonFools
something like, off the top of my head on my phone:

#!/bin/sh
for f in `find $1 -name '*.flac'`; do
mkdir -p somedir # does nothing if dir exists
IN=`realpath $f`
OUT=`$IN.output`
flac blahblah
done

you can customize from there for what you want, more args to the script, etc