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mv $file $newfile >/dev/null 2>&1
...


regards,
Ahamed

I am not sure why it creates the merged file in the main folder.
Anyways you can try this giving the full folder path


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grep '.*' *.txt > $HOMEDIR/$dir/_merged_temp.txt
sed -i...

If you are using the grep and sed command to merge all the file in the subfolder to one big file, then you can try this

#!/bin/ksh
HOMEDIR=/cygdrive/n/test
dirs=`ls | grep -v run`
for dir in...

Try this...
The script is placed in the parent directory where the subfolders are present and ths script name is "run.sh"


#!/bin/ksh

HOMEDIR=/user/ahamed/test
dirs=`ls | grep -v run`
...

sed 's/.*/&,file1/' file1 >temp
mv temp file1