use Prompt::Timeout;
use constant TIMEOUT => 5;

...

if (defined($size_remote))
{
    my $default = ($size_remote == $size_local) ? 'N' : 'Y';
    my $answer  =  prompt('Overwrite?', $default, TIMEOUT);
    
    upload($_) if $answer =~ /^Y/i;    # overwrite
}
else
{
    upload($_);
}

##</code><code>##

while (defined ($_ = readdir($eh)))

##</code><code>##

while (readdir($eh))

##</code><code>##

my $pattern = join '|', map "(?:$_)", @filetypes;

##</code><code>##

my $pattern = join '|', @filetypes;

...

while (readdir($eh))
{
    next if /~$/ || -d || !/$pattern/i;
    ...