Take a look at "Scripts-->@thin leoScripts.txt-->Important-->Write
cleaned files to 'clean' directory" in leo/scripts/scripts.leo.

To see how it works, copy this node to your outline and create a
script button from it.

It just populates your source tree with clean version of your files,
it doesn't create a paralel directory structure with only clean files
like you might need. But at least you can see how it does it. Of
course, if all your @thin files are in the same directory, this script
will suit you fine: it will create a "clean" directory and will put
all clean files there.
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