JavaScript-Minifier é um módulo em Perl usado para minimizar/otimizar arquivos JS.

Partindo do princípio de que já tenha o Perl instalado em seu sistema, o próximo passo é instalar o módulo.

Em Debian/Ubuntu e derivados isso pode ser feito com o seguinte comando:

sudo apt-get install libjavascript-minifier-perl

Nas demais distribuições (incluindo Debian/Ubuntu), é possível instalar o módulo usando o shell CPAN:

sudo perl -MCPAN -e shell
cpan> install JavaScript::Minifier

Leitura recomendada: A forma correta de se instalar módulos Perl [Artigo]

Agora vamos criar o Perl script que será usado para minimizar arquivos JS:

sudo vim /usr/local/bin/jsmin.pl

#!/usr/bin/perl

my $source = shift;

if (! -f $source) { 
	print "Use: $0 <input-file>\n\n";
}

use JavaScript::Minifier qw(minify);

open(INFILE, $source) or die;
print minify(input => *INFILE);
close(INFILE);

Salve e saia. O código, além de ser auto-explicativo, não é o foco do artigo. Apenas transcreva-o e em seguida torne-o executável:

sudo chmod a+x /usr/local/bin/jsmin.pl

Pronto! Já podemos usar o comando jsmin.pl para minimizar nossos scripts. Exemplo:

jsmin.pl app.js > app-min.js

Compare o código original com o código gerado e veja a diferença:

/* app.js original */
/*
 * Template Name: Unify - Responsive Bootstrap Template
 * Description: Business, Corporate, Portfolio, E-commerce and Blog Theme.
 * Version: 1.6
 * Author: @htmlstream
 * Website: http://htmlstream.com
*/

var App = function () {
    //Bootstrap Tooltips and Popovers
    function handleBootstrap() {
        /*Bootstrap Carousel*/
        jQuery('.carousel').carousel({
            interval: 15000,
            pause: 'hover'
        });

        /*Tooltips*/
        jQuery('.tooltips').tooltip();
        jQuery('.tooltips-show').tooltip('show');      
        jQuery('.tooltips-hide').tooltip('hide');       
        jQuery('.tooltips-toggle').tooltip('toggle');       
        jQuery('.tooltips-destroy').tooltip('destroy');       

        /*Popovers*/
        jQuery('.popovers').popover();
        jQuery('.popovers-show').popover('show');
        jQuery('.popovers-hide').popover('hide');
        jQuery('.popovers-toggle').popover('toggle');
        jQuery('.popovers-destroy').popover('destroy');
    }

    //Search Box (Header)
    function handleSearch() {    
        jQuery('.search').click(function () {
            if(jQuery('.search-btn').hasClass('fa-search')){
                jQuery('.search-open').fadeIn(500);
                jQuery('.search-btn').removeClass('fa-search');
                jQuery('.search-btn').addClass('fa-times');
            } else {
                jQuery('.search-open').fadeOut(500);
                jQuery('.search-btn').addClass('fa-search');
                jQuery('.search-btn').removeClass('fa-times');
            }   
        }); 
    }

    //Sidebar Navigation Toggle
    function handleToggle() {
        jQuery('.list-toggle').on('click', function() {
            jQuery(this).toggleClass('active');
        });

        /*
        jQuery('#serviceList').on('shown.bs.collapse'), function() {
            jQuery(".servicedrop").addClass('glyphicon-chevron-up').removeClass('glyphicon-chevron-down');
        }

        jQuery('#serviceList').on('hidden.bs.collapse'), function() {
            jQuery(".servicedrop").addClass('glyphicon-chevron-down').removeClass('glyphicon-chevron-up');
        }
        */
    }

    //Fixed Header
    function handleHeader() {
         jQuery(window).scroll(function() {
            if (jQuery(window).scrollTop()>100){
                jQuery(".header-fixed .header-sticky").addClass("header-fixed-shrink");
            }
            else {
                jQuery(".header-fixed .header-sticky").removeClass("header-fixed-shrink");
            }
        });
    }

    //Header Mega Menu
    function handleMegaMenu() {
        jQuery(document).on('click', '.mega-menu .dropdown-menu', function(e) {
            e.stopPropagation()
        })
    }

    return {
        init: function () {
            handleBootstrap();
            handleSearch();
            handleToggle();
            handleHeader();
            handleMegaMenu();
        },

        //Clients Logo
        initSliders: function () {
            jQuery('#clients-flexslider').flexslider({
                animation: "slide",
                easing: "swing",
                animationLoop: true,
                itemWidth: 1,
                itemMargin: 1,
                minItems: 2,
                maxItems: 9,
                controlNav: false,
                directionNav: false,
                move: 2
            });
            
            jQuery('#clients-flexslider1').flexslider({
                animation: "slide",
                easing: "swing",
                animationLoop: true,
                itemWidth: 1,
                itemMargin: 1,
                minItems: 2,
                maxItems: 5,
                controlNav: false,
                directionNav: false,
                move: 2
            });
            
            jQuery('#photo-flexslider').flexslider({
                animation: "slide",
                controlNav: false,
                animationLoop: false,
                itemWidth: 80,
                itemMargin: 0
            }); 
            
            jQuery('#testimonal_carousel').collapse({
                toggle: false
            });
        },

        //Counters 
        initCounter: function () {
            jQuery('.counter').counterUp({
                delay: 10,
                time: 1000
            });
        },

        //Parallax Backgrounds
        initParallaxBg: function () {
             jQuery(window).load(function() {
                jQuery('.parallaxBg').parallax("50%", 0.2);
                jQuery('.parallaxBg1').parallax("50%", 0.4);
            });
        },

    };

}();

E o resultado:

/* app-min.js */
var App=function(){function handleBootstrap(){jQuery('.carousel').carousel({interval:15000,pause:'hover'});jQuery('.tooltips').tooltip();jQuery('.tooltips-show').tooltip('show');jQuery('.tooltips-hide').tooltip('hide');jQuery('.tooltips-toggle').tooltip('toggle');jQuery('.tooltips-destroy').tooltip('destroy');jQuery('.popovers').popover();jQuery('.popovers-show').popover('show');jQuery('.popovers-hide').popover('hide');jQuery('.popovers-toggle').popover('toggle');jQuery('.popovers-destroy').popover('destroy');}
function handleSearch(){jQuery('.search').click(function(){if(jQuery('.search-btn').hasClass('fa-search')){jQuery('.search-open').fadeIn(500);jQuery('.search-btn').removeClass('fa-search');jQuery('.search-btn').addClass('fa-times');}else{jQuery('.search-open').fadeOut(500);jQuery('.search-btn').addClass('fa-search');jQuery('.search-btn').removeClass('fa-times');}});}
function handleToggle(){jQuery('.list-toggle').on('click',function(){jQuery(this).toggleClass('active');});}
function handleHeader(){jQuery(window).scroll(function(){if(jQuery(window).scrollTop()>100){jQuery(".header-fixed .header-sticky").addClass("header-fixed-shrink");}
else{jQuery(".header-fixed .header-sticky").removeClass("header-fixed-shrink");}});}
function handleMegaMenu(){jQuery(document).on('click','.mega-menu .dropdown-menu',function(e){e.stopPropagation()})}
return{init:function(){handleBootstrap();handleSearch();handleToggle();handleHeader();handleMegaMenu();},initSliders:function(){jQuery('#clients-flexslider').flexslider({animation:"slide",easing:"swing",animationLoop:true,itemWidth:1,itemMargin:1,minItems:2,maxItems:9,controlNav:false,directionNav:false,move:2});jQuery('#clients-flexslider1').flexslider({animation:"slide",easing:"swing",animationLoop:true,itemWidth:1,itemMargin:1,minItems:2,maxItems:5,controlNav:false,directionNav:false,move:2});jQuery('#photo-flexslider').flexslider({animation:"slide",controlNav:false,animationLoop:false,itemWidth:80,itemMargin:0});jQuery('#testimonal_carousel').collapse({toggle:false});},initCounter:function(){jQuery('.counter').counterUp({delay:10,time:1000});},initParallaxBg:function(){jQuery(window).load(function(){jQuery('.parallaxBg').parallax("50%",0.2);jQuery('.parallaxBg1').parallax("50%",0.4);});},};}();

Fonte: http://search.cpan.org/~pmichaux/JavaScript-Minifier-1.05/lib/JavaScript/Minifier.pm

É isso!