The worst thing about long if-elsif-else chains is their performance, but you are talking about an interactive aplication, so you don't need to worry about performance and chained if-elsif-else's will not be so bad.

Anyway, let my suggest an alternative OO aproach: define a class for every command you support, i.e.: MyApp::Command::ls, MyApp::Command::cp, etc.

Then, in every command class define the set of methods you need, i.e. parse_args(), run(), print_output(), etc.

And then use the perl OO notation to dispatch commands:

while(read_cmd()} {
  eval {
    $cmd_name=~/^\w+/ or die "invalid command";
    my $cmd_class = "MyApp::Command::$command_name";
    my $cmd = eval { require $cmd_class; $cmd_class->new };
    if ($@) die "unknow command $cmd_name ($@)\n";
    $cmd->parse_args(@args) or die "...";
    $cmd->run(@args) or die "...";
    etc();
  };
  print $@ if $@;
}
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This way, adding new commands is very easy, just create new classes for them and drop them on the rigth directory. It also allows for simple code reuse via inheritance.