#!/bin/bash

inarray() { local n=$1 h; shift; for h; do [[ $n = "$h" ]] && return; done; return 1; } # Usage: inarray "$value" "${array[@]}"

files=("test" "foo" "foo" "bar" "test")
inc=1
for filename in "${files[@]}"; do
    if ! inarray "$filename" "${filelist[@]}"; then
        filelist+=("$filename")
    else
        filelist+=("$filename""$inc")
        ((inc++))
    fi
done

echo "${filelist[*]}"