Batch processing pandoc conversions

I made a bash script that would not work recursively, perhaps you could adapt it to your needs:

#!/bin/bash    
newFileSuffix=md # we will make all files into .md

for file in $(ls ~/Sites/filesToMd );
do
  filename=${file%.html} # remove suffix
  newname=$filename.$newFileSuffix # make the new filename
#  echo "$newname" # uncomment this line to test for your directory, before you break things
   pandoc ~/Sites/filesToMd/$file -o $newname # perform pandoc operation on the file,
                                                     # --output to newname


done
# pandoc Catharsis.html -o test

You can apply any command across the files in a directory tree using find:

find . -name \*.md -type f -exec pandoc -o {}.txt {} \;

would run pandoc on all files with a .md suffix, creating a file with a .md.txt suffix. (You will need a wrapper script if you want to get a .txt suffix without the .md, or do ugly things with subshell invocations.) {} in any word from -exec to the terminating \; will be replaced by the filename.