Online command line JavaScript optimization
Looks like arguments_to_array() can be removed.

You may want to consider having cli_parse() call cli_remove_blank_words() rather than cli_run().

Also, depending on the direction you're going with the command line, you can probably simplify cli_run() in other ways. That long document.getElementById expression should probably be isolated in its own function, since it seems it's going to be used the same way every time for the most part. By doing shift() to the cmd array, you can get the function you want to call from that (and the remaining elements in the array are simply your args to that function). Then you can use a logical operator to check whether that function exists, otherwise call a function that handles errors and such.

Here's how I'd do it:

function cli_parse(cmd) {
    return cli_remove_blank_words(cmd.split(/\s+/));
}

function cli_run(cmd) {
    var words = cli_parse(cmd);
    var func_name = words.shift();
    var func = window[func_name] || window.cli_error;
    func.apply(this, words);
}

function cli_print(txt) {
    document.getElementById('commandline').value =  document.getElementById('commandline').value + '\n&gt;&gt;&gt; ' + txt;   
}

function cli_error(error_info) {
    cli_print("Unknown command");
}

function add(a,b) {
    var result = parseInt(a)+parseInt(b);
    cli_print(result);  
}


Although, I'd really say using a more object oriented approach would probably facilitate expansion easier, but this works fine.