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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.

Minifying dynamically loaded javascript whilst leaving it editable

So, I am using CodeIgniter to develop a website.
I noticed I had about ten javascript files all being loaded in my header even though they were not all being used on a given page.
As such I now pass an array to my header view which contains a list of the javascript files which need to be included. This way only the files I need on a given page are loaded.
I ran my site through a speed test, and although it is pretty fast it flagged up the numerous JS file loads and said to combine them into one file, and minify it.
I have my JS files as seperate files so I can use them as above, and also so if i want to edit my tabs js, I can easily find it in tabs.js
Combining all the javascripts into one file would remove the benefits above. Minifying them would make them a lot of effort to edit..
Is there a way of combining the JS files and minifying them when the server tries to load them, or any way to avoid the problems above?
Thanks

HTML + JS + CSS converter

I have a HTML file with JS (jQuery) and CSS. I want a converter that converts all the files, minimizes it and just puts it all in a index.html for example. Google seems to be using this, they have no external files, not even the image, everything is just in one file and I'm sure pre-compiled before release.
Also is this a good idea?

This is not a good idea, in general.
Splitting out your CSS and JavaScript files means that they can be cached independently. You will likely be using a common CSS and JavaScript across many pages. If you don't allow those to be cached, and instead store them in each page, then the user is effectively downloading a new copy of those files for every page they visit.
Now, it is a good idea to served minified versions of these files. Also make sure to add gzip or deflate transfer encoding so that they are compressed. Text compresses nicely... usually around a ratio of 1/8.
(I should note that there has been one occasion where I have loaded everything into a single file. I was working on a single-page web application for the Nintendo Wii, which had no caching capability at all. This is about the only instance where putting everything into a single file made sense. Even then, it is only worth the effort if you automate it server-side.)

I don't recommend to concat CSS with JS.
Just put your css at the top of the page and js at the bottom.
To minify your CSS and JS you have to use gruntjs
Also I recommend you to read this article: Front-end performance for web designers and front-end developers

If your intention is to load the pages faster:
For images: try to use image sprites or images from different domains because browsers love downloading resources from different domains instead of just one domain.
For scripts as well as css: use online minifiers that can reduce white-spaces and reduce the size (if you are on a web hosting, your host may be already compressing the scripts for you using gzip etc)
For landing pages like index pages: If you have less styles then try inserting them inside the <style></style> tag, this will make the page load very fast, Facebook mobile does it that way.

If it wasn't a good idea, google wasn't be using it!
If you put everything in single file, you'll get less HTTP requests when the browser will check if the newer version of file is available.
You also get read of the problem that some resources are not refreshed, which is the headache for 'normal' developers, but it's a disaster in AJAX applications.
I don't know of any publicly available tool doing it all, surely Google is having its own. Note also that, for example in GWT, many such embedding was done by compiler.
What you can do is to search for:
CSS image embedder - for encoding images into CSS
CSS and JS minifier - for building single CSS/JS and minimizing it
And you need some simple tool that will embed it into HTML.

HTML5 Boilerplate Page-specific Javascript Placement

Question
If you use a single javascript file to hold all scripts, where do you put scripts that are for just one page?
Background
This may be a matter of opinion or "best practice" but I'm interested in others' opinions:
I'm using the html5 Boilerplate on a project. They recommend you place all javascript in a single file script.js for speed and consistency. Seems reasonable.
However, I have a bit of geolocation script that's only relevant to a single page, and not others. Should I break convention and just put this script on the page below my calls to the javascript libraries it depends on? Just put calls to the relevant functions (located in the script.js) file, below the links to the libraries they depend on?
Thanks!

The good folks at html5 boilerplate recommend putting all of your javascript in script.js so that the browser will only have to load that one file (along with the others that h5bp uses) and to allow caching of that file.
The idea is not to get caught up in the "recommended" way, and to think about things related to your own applications.
This geolocation file is only going to be used on this one page, right? It will never be used anywhere else.
The script.js file will be used on multiple pages.
Well, then it wouldn't make sense to put a "whole script" that will only be needed on one page in the script.js file. You should make the file external and call it separately on the page that it is needed. This will keep you from bloating the script.js file for functionality that may never get used by that user.
However, if your "whole script" for the geolocation functionality is pretty small, then include it in script.js. If it doesn't add to the speed of the download for that file, then it makes sense to include it there.
The gist of all of this is, What is the best trade off for my application?
These things we know to be true:
cached js files are good
fewer files to download are good
smaller files to download are good
maintenance is important
Once you think of these things in terms of your application, the decision making becomes a bit easier. And remember, decisions that trade off milliseconds are not going to make much of a difference in your user's "perception" of how fast your page is.

The browser will only download the .js files once (unless something is happening to discourage the browser from caching). So if you expect all of your users to hit the one page that uses geolocation sometime during their session, then you might as well give it to them early. If you expect maybe a tiny percent of your users to eventually hit the geolocation page, then maybe you might want to split them.

Split it out into a separate .js file so that it can be cached. Then reference both external .js files from your page.

I think you should put it in a separate file. Putting all the scripts in one single file could cause unexpected behavior and conflicts. I like to have one script file for the javascript that all pages will use containing plugins, helper functions, formatting functions etc. And then create one separate js file for everything that is relevant just for each page.
If you still want to have just one js file in the browser you could take advantage of one of those utilities that combine multiple js files into one.

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.