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Con una versión reciente de bashque maneja arreglos asociativos,lo siguiente también manejaría nombres de ruta con líneas nuevas incrustadas:

#!/bin/bash

topdir=$HOME

shopt -s globstar  # enable the ** glob

declare -A count

# count the number of times each filename (base name) occurs
for pathname in "$topdir"/**; do
    # skip names that are not regular files (or not symbolic links to such files)
    [ ! -f "$pathname" ] && continue

    # get the base name
    filename=${pathname##*/}

    # add one to this base name's count
    count[$filename]=$(( ${count[$filename]} + 1 ))
done

# go through the collected names and print any name that
# has a count greater than one
for filename in "${!count[@]}"; do
    if [ "${count[$filename]}" -gt 1 ]; then
        printf 'Duplicate filename: %s\n' "$filename"
    fi
done

Esto no utiliza ninguna utilidad externa.