Dont use base64, but hex.

The hex-decoder can be made so it does not need to be quoted.

# Input:                                                                                                                     
#   zipper space Base64 16384*space \n                                                                                       

my($zip,$base64);
{
    my @b;
    my $kb8=" "x8192;
    # Read most in blocks of 8 KB                                                                                            
    while(sysread(STDIN,$buf,8192)) {
        if($buf eq $kb8) { last; }
        push @b, $buf;
    }
    ($zip,$base64) = split / /,join "",@b;
    # Read the final partial block byte by byte                                                                              
    # to avoid reading too much from STDIN                                                                                   
    while(sysread(STDIN,$buf,1)) {
        if($buf eq "\n") { last; }
    }
}
print $zip;
$dec = decode_base64($base64);
if($zip) {
    # filter $dec through zipper                                                                                             
    $dec = $dec;
}
eval $dec;

Make a perl wrapper that:

reads 1 line of Base64 encoded perl script. Executes the script.

This will make it possible to ignore the csh limitation of word length and the bash limitation of line length.

It should be compatible with --pipe, so the wrapper should pass the rest of STDIN to the --pipe command.

Does it make sense to bzip2 the script when running remote? How long does it take to bzip2/bunzip2 compared to transfer time? Without the bzip2 it will make it easier to simply run the same unpacker locally and remotely. Alternatively the Base64 line can be prepended with 'bzip2' if it needs to be bunzipped.