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How to detect when the last file of the manifest file is updated?

I'm building an Offline HTML5's App, which has several pages inside (10 to be more specific). When I need to change any of these pages, I simply change the manifest file to instruct the browser to update all files (As the HTML5 documentation recommends). But here is the problem that nobody talks about:
While the browser is downloading the files, my dear users rushes into the app and start using it, then they complain that the changes did not take place. After hours of testing, I realized that the browser is slower than my users. So here is my question:
How to detect when the last file of the manifest file is fully updated? or in other words, how to stop my user to stop using the app until the last file in the manifest is fully downloaded?
I don't find anything on the Web about this issue
Is there any Javascript?

Listen to the cached event in the application cache API.

source code changes do NOT reflect immediately upon uploading them on my web host

This is not a programming question per se. I am using a free web host called getfreehosting. I am using their online file manager to transfer files. From time to time, the changes I make on source code do NOT reflect immediately after I upload them. I.e. when I run my application on Chrome, then go to view page source, I realize the JavaScript running is still the old version! In most cases this doesn't happen but when it does it is extremely frustrating. I've tried clearing the browser's cache. I even tried editing the file directly on their servers. Sometimes it solves the problem but other times it doesn't.
Is this a common issue encountered when transferring files to a web host? Or perhaps this is one of the downsides of using a free web host?
Thanks.

You can try clearing your browser's cache, or the ol' CTRL+F5 refresh trick. Otherwise, the hosting provider may be using a caching layer to help ease resource usage.

It is the responsibility of the server to indicate to the browser what the cacheable lifetime of the script files are when they are served to the browser (1 hr, 1 day, 1 month, etc...). This is a server side setting.
Caching is very important for both server-side efficiency and client-side performance so you don't want to defeat it completely.
You can either shorten the server-side setting for the cache lifetime or you can use a version number in your script files (like jQuery does) so that when you revise your script files, you give them a new filename like "myscript-v12.js" and update the corresponding HTML files to refer to the new filename. Then, as soon as the browser gets the new HTML file, it is guarenteed to get the new JS file because the new filename could never have been in the browser cache.
If this is just an issue for you personally while developing and revising your site, then just clear your browser cache after you upload new files and then when your browser loads that page, it won't have any version in the cache and will be forced to get the new version from the server.

There is a CACHE system in modern browsers.
Try clear cache before you browse your web site.

HTML5, "bypassing" localstorage settings

In a web application I'm creating a lot of media is used. As such there's quite a strain if each time the page is loaded this media has to be loaded again. (And as the media isn't inside the page, but rather retrieved by means of websockets I doubt the browser will cache it).
As such to protect both the server & the client, and to prevent useless strain on networks I wish to "store" the media locally - and then simply load each time the program is run. Now the big problem is, localstorage (which seems to be made for this) is very, very limited: 5Mb in firefox. That's by far not enough for the media my program will use (around 100Mb) - it's also weird to me as nowadays we have hard drives of several terrabytes?
Is there a manner to "ask" for more local storage (apart from telling people to fiddle with about:config or similar things). Or otherwise, can I download this media and then load this local data? (Can I KNOW where the user has downloaded the data without the user manually navigating to the data?)

The newest browsers support, one way or another, an application cache. It is intended to allow offline access to the resources a web-application fetches from a server, and does not use the localStorage memory space.
http://html5doctor.com/go-offline-with-application-cache/

Versioning Javascript Files to Prevent Unnecessary Cache Clearing

I version all of my client side JS files like "/js/myfile.js?v=3903948" so that my clients don't need to clear their browser cache to ensure they get the updated files. But every time I push an update, without fail, at least one person runs into a problem where they are running the old version and get some kind of error. I used to think that this was just them having already been on the page during the release and just needing to reload the browser, but this happened to me today when I was definitely not previously on the page. I browsed to the live site and was running the old code. I needed to do a browser refresh on that page to get the new file.
What can cause this?
PS I was using Chrome on Win7, but I have seen clients report this before on all different browsers.

If your main web page can also be cached, then the old version of that page can be requesting the old version of the JS file. JS file versioning works best if the page that actually refers to the JS file cannot be cached or has very short caching time.

I agree with jfriend00 about the webpage itself being cashed and thus requesting the old javascript version.
To prevent this, you can have the javascript file loaded by an ajax (Post) request, either requesting the server what is the accurate(latest) version number to download, or requesting the javascript itself and inserting it, e.g. in the head of the page.
Edit: see for example here

I make a quick AJAX request to the server for the version it expects them to have, then force them to refresh the page if the client's script is old.

Seems that proxy or some load balancer is serving old content instead of new. Also check IIS/webserver settings how are these files cached/expired.
You can check what is going on on the wire with tools like Fiddler.

Detecting if a browser's cache is full

We've identified that full browser caches are the cause of a problem on our extranet. It only affects a small number of our users, but we'd like to alert them to the problem and give them some guidance on how to fix the problem for themselves.
We'd like to use a similar system to the one which GMail uses. When it detects that your browser's cache is full is not behaving as it should, it shows a warning message telling users that their cache is full and that it may cause problems with GMail, along with a link to a Gmail Help page on clearing your browser's cache.
Does anyone know if there any resources out there, or examples of how to use JavaScript to detect that the browser's cache is full behaving badly?
Thanks.
Clarification: What we're actually trying to detect, I suppose, is not whether or not the cache is full, but rather whether a script, which we have configured server-side to be stored in the cache, is being re-requested from the server - in such a way that the browser is behaving strangely, or as if its cache is not behaving as it should.
Further Clarification: Thank you all for the updates on caching. Our scripts are being sent with the correct headers, and we're only seeing this problem in IE6 and IE7 - Mozilla and WebKit browsers seem to be unaffected - but I'm still not sure on how exactly we'd go about using JavaScript and/or XmlHttpRequest to check to see whether or not an object was retrieved from the cache, thus letting us check whether the cache is behaving badly.

The browser's cache will not cause problems if it is full... with a few minor notes.
If the browser cache is full, the browser simply has to download fresh content vs. pulling it from its local cache. (e.g. is slower)
If the browser cache contains invalid data (e.g. an old copy of a JavaScript file) then yes, you may encounter issues. (not because the cache is full, but because you didn't serve up a fresh file for the user (Google for: expires headers and how to alter the URL path to your files when you make script changes to ensure you "break" the cache))
In Internet Explorer, when you push a download file (e.g. an Excel spreadsheet) to the user it must go into the cache to work (an IE bug) - I'm not sure if the file is bigger than the users' total cache, if that causes issues with the file being stored, and therefore loaded (Stackers pls feel free to confirm if this one way or another)
Update:
Based on your clarification, you need to ensure that any script you send to the client is appropriately cached... which means:
Change the URL to your scripts when you want a new version to be downloaded (e.g.)
http://example.com/scripts/latestThing.js?ver=3425
where the "ver" is pulled from your versioning system to ensure you always force the browser to download a fresh copy any time you change your script.
Once you are sure that the URL changes, you can send cache headers that tell the browser to cache the files for a very long time (e.g. your JS Library files (e.g. jQuery) likely don't change every hour, day, week or even month)

This will probably not work as is. But its just an idea:
var img = new Image();
(new Image).src = "imageWithFarFutures.png";
window.onload = function(){
document.getElementById("someIframe").src = "imageWithFarFutures.png";
// NOW if the server DOES get a FRESH request for "imageWithFarFutures.png"
// wouldn't it mean that the browser has kicked it out of its cache?
};

Consider sending a header to have your application never cache your content and to have it expire immediately.