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Whatever you mean by "nested" - yes, commands do behave identical, be they issued on the command line or run within a script.

man ls reveals that there is a -r option. Alternatively you might want to look into the find command.

Your Welcome. Then your ls should know -S

I would suggest at the end within the if cd /Users/christopherdorman/desktop block

Try, then,
read -p "Good Morning, Please enter your file type name for sorting [ENTER]:" all_extensions
if cd /Users/christopherdorman/desktop
then while read extension
do...

Perhaps, the following might be a guide:

#!/bin/bash

echo "Good Morning, Please enter your file type name for sorting [ENTER]:"
read extension
mv -v...