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Could someone explain how I can combine my JS and CSS files?

I have done my research on combining JS and CSS files. I am still a novice when it comes to all of this so the explanation like some of these minifies and compilers at Github and Google don't really make sense in normal English.
I have the following CSS files:
bootstrap
bootstrap-min
bootstrap-responsive
bootstrap-responsive-min
main
prettyPhoto
These are my JS files:
bootstrap
bootstrap.min
jquery
jquery.prettyPhoto
jquery-migrate-1.2.1
theme
Which tool should I use and if someone could explain step by step that would be great.

If you want to just have one big js and cs file then you can just combine them into ones by copying and pasting the content of each file one after another, in the same order you would include them on a page. Keep in mind that you do not need bootstrap if you are including bootstrap.min file after it. It's the same file, only the one with .min in name is minified version of it. Same goes for js files.
Then if you want... you can run a tool for compression like this one:
http://refresh-sf.com/yui/
and hope everything works fine.

Though combining files is easy that not something you should do to libraries. Moreover for most cases you should not merge these files.
Libraries tend to stay unchanged for long time, thus will be eventually cached by user. Site loading time will be faster.
A good approach is to link these libraries to 3rd party CDNs (Google, JQuery, etc.). They are far better with load balancing and this will increase your page loading time. (There could be some DNS lookup overhead, though).
Larger files tend to skip the cache. So having large file can make your page significantly slower if every next page call will download the library again.
Of course for your custom script joining in single file and minimization will almost always be recommended.

combining javascript files

I've launched a redesign of our website and I'm using quite a bit of Javascript for the first time.
I've learned that I should be combining all my javascript and css into one file (each obviously) but while I know I can combine the css without problems but the javascript I'm not sure of.
I have to load:
jquery.min.js <-- I load the top two from ajax.googleapis.com, is that a good idea
jquery-ui.min.js
javascript for Facebook
some for google plus button
same for twitter
some for google analytics
then some inline stuff to hide divs which javascript users shouldn't see and that type of thing.
you can see it here: traditionalirishgifts.com
So can I just copy and paste the contents of all these files into one big file. Find some way to minify (haven't looked into that fully yet) it. Load this one file right at the bottom of my page before and bingo?

I'd use this tool: http://jscompress.com/
JSCompress.com is an online javascript compressor that allows you to
compress and minify your javascript files. Compressed javascript files
are ideal for production environments since they typically reduce the
size of the file by 30-90%. Most of the filesize reduction is achieved
by removing comments and extra whitespace characters that are not
needed by web browsers or visitors.

You should always be able to merge all your external JavaScripts into one file. You can use a server-side compressor to cache it and serve it as one file. It does put some constraints on the files, like which file should load first etc. Also, if there is a syntax error anywhere it will crash completely.
Keep in mind that 3rd party code like code from google can't be mixed in. Usually there is some kind of authentication going on (or an API key in the URL). If you try to cache that code, it will stop working after a while. So you do need to keep those separate.

Include separate CSS and JS files into the header OR all code in one CSS and one JS file?

I'm trying to optimize my website. I have a few plugins to include (jquery plugins with CSS), and my own javascript code.
Now I have the CSS in separate files for different plugins, as I downloaded them. And if I need one on the actual page, I generate code to include that. The same with the JS files. But when it comes to render a complex page with a lot of stuff, 9 CSS files can be called and 7 or 8 JS files, each of which are HTTP requests.
Should I put the CSS into one big file to reduce the number of included CSS files? But then everything will be interpreted by the browser even if the current page doesn't need so much stuff.
I've thought of a third way: generate CSS and JS files with PHP. Then it'll be always one JS and one CSS file, and only with the things which are needed. Or is it an absurd way?
What do you say, which to use to reduce page load time?

It is better to include all CSS in a file and all JS in a file and the minify them using many online services that minify and compress CSS and Javascript. this will reduce the number of http requests as well as volume of data to be downloaded.
If you generate CSS with php then the CSS and JS should be downloaded with every page and generating them takes some time, but if you pack them in one file it downloads once and the browsers caches it.
if your site has many different sections and packing all css in a file makes a huge file then you can pack CSS in two or three file and in each section load the related one.
reducing number of http request is very important.

I think your last solution is the best one.
Generate one js file and one css file from php, and don't forget to minimized/gziped them :)
Here is a very good article about optimization : http://developer.yahoo.com/performance/rules.html

This depends largely on how your users use your page. If most of the users just view one page then it makes sense to only send them the stuff that they need to display that one page (combining everything into as few requests as possible). On the other hand if most of users view multiple pages then it makes sense to send them more than they need so they will already have the CSS&JS on the next page view. But in this case you have to make sure that you are always generating the same CSS&JS with the same URI, so that the browser will not re-download the same content under a different name. You also have to setup proper HTTP caching.
What I usually do is split JS/CSS in two parts. Every page has a "common.css" and "common.js", which has stuff that every page needs (header/footer/... styles for CSS, and then jquery/common js/... for JS). Then every subpage has it's own JS&CSS that has just the stuff you need for that page (if required).

For me, the best way is somewhere in the middle - for CSS files, you better grab them all, join and compress to one file. For JS code - make for example 3+ files: one with compressed and joined external libs, one with your common stuff, and maybe next files for each bigger section - but I dont think its needed. Maybe splitting your JS code on part needed before user login, and after user login.
Remember to minify and consider asynch loading (with LAB.js for example).
Oh, and this php script... I dont think it is good idea - better use/write some script which joins and minifies your statics on compile (or deploy, or even run by hand), so there is no need to generate everythin over and over again.

References Asp.net JS files

I have a notepad filled with references to over 1k .js files. I would like for my page to check this file and add each as a reference eg:
<script type="text/javascript" src="####.js"></script>
any idea or examples on this.
Thanks

Not a direct answer to your question, maybe, but if you reference that many files maybe you should look at the Google closure compiler, or the Dojo build system, or search for javascript minifiers?
In addition to your page loading faster, you won't have to generate all those links.

Also not a direct answer, however you could simply create a control which is entered into your asp.net masterpage in the header and geneates your script tags.
However by itself that's going to cause serious performance problems with your website having references to so many javascript files.
I would serioulsy recommend that you look into using the AjaxToolkit (or other frameworks) to merge and minify all of your separate JS files into 1 file that gets generated dynamically.
The example I have below is for both CSS and JS which does minification and compression on the fly.
https://softwareengineering.stackexchange.com/questions/98810/how-to-organise-website-css/98818#98818

Where to place my JS code and where/how to load multiple jQuery plugins?

I have a couple of questions that are somewhat related so I'm posting them all on a single question on SO...
Question 1:
I'm currently doing this Facebook application where I'm using jQuery UI Tabs, there's only 4 where 2 of them are loaded through Ajax. The main page is index.html, this is where the tabs code is placed and for the 2 tabs loaded through Ajax, I have two different files, tab1.html and tab2.html.
Currently, the jQuery tabs initialization and Facebook JavaScript initialization is done on index.html. Both tab1.html and tab2.html have JavaScript code that belongs to those pages. For instance, tab2.html has a form and there's some JS (with jQuery) code to validate the form, this code is irrelevant to tab1.html as the JS code on tab1.html is irrelevant to tab2.html.
My question is, should I keep doing this or maybe aggregate all the JS/jQuery code in index.html, tab1.html and tab2.html in a single global.js file and then include it in index.html?
I though of doing this but there will be irrelevant code loaded if the user never opens tab1 or tab2. The benefit of using a single global.js file is that I could pack/minify the file, which I couldn't do if I included each code block in each respective tabX.html file.
Question 2:
As I'm using jQuery, I'm also using lots of plugins (actually only 3 for now, but that number can grow). Some of them provide a minified JS and I use those when available, when they are not, I use the normal versions of course.
There's also the requests problem. If I have lots of plugins, say 10, it will be 10 requests for those plugins. And there is also the fact that some plugins are used in tab1.html but not on tab2.html and vice-verse.
How should I load all the plugins in a minified/packed version on a single web request? Should I do that manually before publishing my app (packing and merging them into a single file) or could I use the PHP version of Dean Edwards's Packer and pack/merge all plugins on the fly? Would this be a good approach?
Question 3:
If the answer on Q1 was something like "merge all code in a single global.js file", should I include the global.js file in the packing/merging script I described above on Q2?
Doing this would simplify everything. I could have my development environment properly organized with all .js files, for the plugins and the global.js in the appropriate folders without bothering with anything else. The packing/merging should take care of the rest (pull the files from the respective folders, send the respective JS headers and output one single packed .js file).
The one thing that's confusing me the most is that not all plugins are used for every tab, not all code is for every tab too. Still, a chunk of the code is global to every tab and the index. This also simplifies everything as: a) I don't have to worry to add the needed code to each tabX.html file and can I simply look at them as HTML templates and nothing else; b) I don't have to be bothered in including the necessary plugins where I need them as I'm currently using $.getScript() from jQuery to load the plugins I need when and only when I need them, but I'm not sure this is a good approach and the code feels dirty and ugly like this.

Question 1:
Pack them all into a single .js file. This will make maintenance easier, and the tiny bit of overhead for the user loading a little js they they potentially may not use does not matter. I would also let Google load the jQuery library for you and then have all of your js code in a single separate file.
Question 2:
As these plugins don't really change I would manually combine them. Closure Compiler is good at this. When minifying use the highest setting that does not give any warnings.
Question 3:
Yes you will want to minify the global.js
When the browser downloads the global.js it's cached for an amount of time. Thus when you call the entire global.js again on a different page, its not re-downloaded it looks at your local copy first. So you do a little bit more work at first on the initial download, but from then on, it should be quicker.

Generally best practices related to javascript for speeding up website loads are:
Minify all javascript and put all of it into a single file (make as much of your javascript external as possible).
Put javascript at the bottom of the document.
Force web server to assign expiration date in the future and use a timestamped query string to invalidate old versions of javascript files, this will prevent unnecessary requests for your javascript if it has not changed. (ie: in httpd.conf ExpiresByType application/x-javascript "access plus 1 year", in your document: <script type="text/javascript" src="/allmy.js?v=1285877202"></script>)
Configure your web server to gzip all text files.

The main reason why you should keep too much javascript away from tab pages is because it will kill user experience. When a user clicks on a tab for the first time it will grab all the components needed on the fly which makes it kinda sluggish.
You're question is only semi-specific as we don't know a lot of things about your site like exact file sizes, how the modules are really used.
The general idea would be to find balance between modularity and speed.
When you're combining modules together these are the general ideas you should consider:
how often does this module change?
how often is this module used?
how big is this module (filesize)?
Then put the most used, stable codebase and merge it into one. Then you should include the rest site specific functionality on the tab pages.
Also, make sure to load javascript asynchronously as it won't block rendering of the page (and tabs).

Another combined answer:
if adding all the JS together in packed/minifed version generates no more than 30k of file size you're better off combining it. A single extra connection for a file (assuming it's not cached) is worth 10-20k of extra JS download. This has to do with browsers opening and closing connections vs streaming extra 20k on an established connection. The threshold also depends on your user distribution. If you have a lot of dial-up or low bandwidth users your threshold will be smaller.
I typically recommend combining and loading as 1 file unless the library is very obscure and requires a very edge case for it to be triggered on a page. Ex: Hover triggers functionality Y but it's on a feedback widget that gets less than 1% of traffic- don't bother combining.
Minifying and Packing is a little overrated these days. With the vast majority of browsers supporting gZip the amount of data consolidation gZip provides of the file over the wire during browser transmission has virtually the same effect as min/pack. However, there is a small cost on the browser to unpack it. Having said that, it's still good practice to min/pack the code since not all browsers support it, you may not want the file to be gZip enabled, etc.
I've used online packers against 3rd party module and it works fairly well. However, there are times when it can cause an issue so make sure to test your manually packed version before deploying.
Alternate:
If you feel that your users will rest on your index page for longer than 10 seconds you could pre-load the additional libraries separately using Js Loader Prototype pattern.

Steve Souder's Even Faster Websites is a book you should look into.
Firstly one experience slowdowns because whenever an external script is linked the browser waits for the script to download, parse and then execute. After this only it regains processing rest of the request. So to avoid such slow downs one can look at parallely downloading the scripts. Few techniques are Ajax the scripts if the scripts are in the same domain or use Script Dom element or Script in iframe if the scripts are on external domains
Q1 : For me modularising all the content is a better option with respect to further development if the page content has to be changed constantly. Responsiveness is very important for the end user. A small global.js will help in getting the app up and running.Parallely one can download the tabX.html.
Q2: As the jquery plugins rarely change. The plugins for the tabX.html pages can be downloaded parallely and locally cached so when the tabX.html is loaded the required plugins need not be fetched. SO all the plugins required by the main page should be in one single file and the ones used by the tabX.html's should be in different files.
Q3 : its a personal choice here. Do you want it to be developer friendly or user friendly. I bank on user friendliness. Making responsive and efficient apps is our job !!!. All the advantages of packing everything into a singe files is you will have ease in development. Well ugly code begets beautiful apps :). Users are speed-aholics. For eg. when google changed its 10 results per page to 20 they saw a considerable drop in search queries. So my opinion is not to pack all of them into one and load each parallely
some of the techniques and relevant links on testing each:
XHR eval /ajax : http://stevesouders.com/cuzillion/?ex=10009
XHR Injection : http://stevesouders.com/cuzillion/?ex=10015
Script in Iframe : http://stevesouders.com/cuzillion/?ex=10012
Script DOM element : http://stevesouders.com/cuzillion/?ex=10010

Question 1:
The best practice would be to place all js files in a single "global" file. This minimizes your HTTP Requests. Let's say you have 5 plug-ins, this would me you need to do 5 request, wherein if you combine them as one, you only need to request it once. This might be a little bit heavy on the first load, but the next time around this file will be cached by the browser, so..no worries about the size. HOWEVER, be careful about the sequence of the scripts when combining it. (I.E. : JQuery script should be placed first on the js file before JQuery UI's)
http://articles.sitepoint.com/article/web-site-optimization-steps/4
http://code.google.com/speed/page-speed/docs/rtt.html
Question 2:
You can do it manually or automatically.Dean Edward's Packer is a good choice. If you're using ASP.NET, you can check MB Compression Handler, if you're using APACHE with PHP perhaps you can change the configuration of your htaccess to gzip it
Question 3:
It'd be better if you pack the "global" javascript file as well. This could save up bandwidth and save more time to load. You got the point, combining all the js files you need for the site will save you time from including individual scripts.