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maybe smthg like :

( find ./@(sourceA|sourceB) -type f -prune) | grep -f textfile | while read a
do
cp $a target/${a##*/}
done

OK, maybe I should have said: That is bash shell code, not POSIX compliant shell code, so it will only work in bash or maybe ksh93. :)

---------- Post updated at 10:22 ---------- Previous update...

Simple
while read file
do rm -f FolderB/$file
done < <(ls FolderA)

for i in FolderA;do
ls ${i}/* | while read file;do
tfile=`basename $file`
if [ -f FolderB/${tfile} ];then
rm FolderB/${tfile}
fi
done
done

#!/usr/bin/env ruby -w

require 'fileutils'
Dir["./A/*"].each do |d|
name=File.basename(d) if File.directory?(d)
if File.exists?("B/"+name)
print "#{name} exists in #{"B/"+name}\n"
...

in ubuntu, you should be able to diff the folder directly.

diff /path/to/FolderA /path/to/FolderB

#!/bin/sh
vr=$(ls /path/to/FolderA)
for fl1 in ${vr};do
echo "${fl1}"
done

vr2=$(ls /path/to/FolderB)
for fl2 in ${vr2};do
echo "${fl2}"
done

Now make two arrays to save the...

Try this:

while read -r line
do
printf "%s\n" "$line" | cat fileB - > "$line"
done < fileA

Try something like this:
i=1
while read -r line; do
printf "%s\n" "$line" | cat fileB - > file$i
i=$((i+1))
done < fileA
or
i=1
while read -r line; do
cp fileB file$i
printf "%s\n"...