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#!/bin/sh

# This will let 'read' eat the carriage returns
IFS="$(printf " \r\n\t")"

while read FILE
do
( # Read the header, and the blank line
read HEADER
...

What precisely is it doing or not doing, that it's supposed to do, or not do? If the computer can't figure out what you want from the malfunctioning code, neither can we unfortunately. You'll have...