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Clicking on Links and Buttons shows focus outline

I am trying to fix a problem in an existing application that uses jQuery. The issue is that whenever I click on any link or button on the page, I see that element take a focus outline (e.g. blue glow in case of Chrome/Safari), as if that element has focus. I have to get rid of that outline after click. I do not think this is a default behavior since I am not able to replicate it on any other site. For that matter, I am not able to replicate it on a simple HTML page that has just one link.
I can not use outline:none
since I have to show the outline in case of focus using tab keys. I have tried using document.activeElement.blur() and $(element).blur() to no luck since some of the event handlers are using event.stopPropagation() and I can not go and change the code for every event handler.
Can anyone please help me with this? What could be the reason a link is retaining focus after clicking? There is nowhere in the code this is being done programmatically since its happening on every single link and button and also some li elements.
Appreciate your help in this regard.

I think that's the default behavior of Chrome and safari.
If you visit this page https://www.linkedin.com/ and click on the Email address and password field then you will see the same thing which is happening with you. I hope I am not wrong..

you can give outline:none;
for the focus/blur on the element: you just add the class .outlineborder
.outline{
outline:inherit !important;
}
$('.button').on('blur').... $(this).addClass('outline');

Understanding focus on divs

I feel like I understand focus():
When trying to focus on a form element, like input, it "just works", so long as the document is ready.
When trying to focus on a non-form element, like div, you must add a tabindex attribute.
tabindex adds the ability to tab to an element in precedence order (higher number the better), 0 and up. However, there's a special value, -1, that explicitly removes the element from the tab order.
When calling focus programmatically, do so within a setTimeout.
Be sure to make a setTimeout value large enough that it waits for display animations to finish, but not so late that the user has time to do other things, like click or type elsewhere.
Pretty simple, really, right? But no. It just doesn't work for me.
My specific use-case is that I have a key-nav-enabled widget that, if you hit the right key, opens a pop-over modal widget. It works great. But I can't get that modal widget to take focus. That modal widget that has no form inputs (just some text and a close link). I've added keydown/up/press events to the modal widget, I've added tabindex to various nodes and tried to focus them, but the original widget still gets the keyboard events.
DOM-wise, the modal widget, despite being new'd up within the keynav widget, is attached to the DOM at the body level, so it's not like the keyboard events are bubbling up through my modal dialog and should be stopPropagation'd, it's never getting those events.
What this means is that if you hit another key before you click in the modal widget, it opens a different modal dialog underneath the first modal dialog!
I really hope I'm missing something about focusing divs, because I have several pieces of functionality I'd like to implement that just aren't working due to (I believe) focus requests simply being ignored.
Help! What am I missing?

In the specific case I was sleuthing out, I effectively had a typo.
I was doing this, which wasn't working:
setTimeout(lang.hitch(this, this.domNode.focus), 100);
But this worked:
setTimeout(function() { this.domNode.focus() }, 100);
That said, I've had a number of issues with focus that regularly make me dread ever having to use it programmatically.
Hopefully though, the list of tips in the question will be helpful to someone.

HTML simulate textarea with div container

I want to create a little WYSIWYG editor.
The idea:
First I want to add the feature to write and change text. So I add an onClick and onKeyBoard Listener to my div container. When I click the div I set a varaible named "focused" to true. When an key event is fired I check if focused is true. In case focus is false nothing will happen else the new charater will be added on the cursor's position.
My questions:
Is this the right way? I tried to check how other editors handle the text input but I wasnt able to get it.
In case this is the right way - how can I simulate a blinking cursor. In a textarea the cursor will blink but who about a div container? The cursor will hide immideatly after clicking.

I'm assuming you're doing this for fun/practice. If you're doing this for professional reason then I HIGHLY recommend you don't reinvent the wheel and use something like Ckeditor, tinyMCE or YUI.
That being said; you need to look into event handling. Specifically, for your question about focusing, you can look here. The way you're describing (setting a variable to true/false) seems like it is going to just run into problems. If you use the standard events attribute (as opposed to setting a "focus" variable onclick) you should define functions to execute and then set them as an onfocus/onblur attribute for the element you're listening to.
That is if you aren't using a javacript library like mootools, jquery, extJS, etc. If you're using one of those they likely have their own way of handling events, so you should search their respective documentation for how to implement event handlers.
One more note; you really should be using a textarea over a div (unless I'm misunderstanding and you just want to do something when a user focuses on your div). If you're using javascript only to completely reinvent a texteditor from a div; then your web page will not function without javascript. If you keep the text area; users could still type information in and you still get the benefit of grabbing text contents for form submits but using divs means your web page will just be rendered useless without javascript.

Debugging issues : detect where my focus is with jQuery?

Forcing focus() on an element is easy, but after having debug issues, I realize trying to determine where is my focus gone is a lot harder.
The thing is I'm generating a modal window using jq.UI, and from time to time, while focus is supposed to be set on first input of the form included in the modal, cursor just disappears, to never show again unless I reload the page.
Is there a straightforward way to detect where my focus/cursor is?

You can see which element it's on by checking document.activeElement, for example:
alert(document.activeElement.innerHTML); //see the content to aid in IDing it

I'm not sure if the focus event bubbles, but if it does, you could try this:
jQuery('body').focus(function(e){ console.log(e.target); })

Javascript context menu click event/detection - filter paste content

Scenario: I'm trying to intercept paste events inside a textarea/input text, and filter the content being pasted.
Webkit/IE are handled rather well, as I can attach code to the onpaste event, and then read from the clipboard what is being pasted. Plenty of examples around.
Gecko is trickier, because as far as I know it isn't possible to read the clipboard content on Firefox (unless somebody knows a workaround for that?)
I just use the input swap trick for that.
Opera is being annoying tho. I can trap CTRL+V and SHIFT+INS, but there's no onpaste event.
Not to mention any sort of clipboard interaction, apparently.
So, my question is:
Can I detect if the user clicked on paste in the context menu on Opera? Is there any other way to detect the event?
EDIT:
Thanks everybody for the answers - they all add a good input, even if there's no definitive solution.
Having to choose, I'll pick the only one that tried to address the original question, and that would probably work if it wasn't too much of an hack to even try.
Notes for those that have my same problem (input filtering):
it is possible to capture content being dragged: mouseup + setTimeout does the trick everywhere almost perfectly.
without flash, there is probably no solution bar polling. Even with flash, it's not a completely solid solution either. Too much effort to support 100% of the cases.

I ran into this last year. In short, no.
I ended up using an onchange handler and filtering the content after it's already been pasted into the text box.

You can intercept the paste with jQuery using the bind('paste', function() {});, compare string before and after pasting and apply your formatting.
The following was tested in IE7/FF3.6/Chrome/Safari 5
$("#textarea").bind('paste', function(e){
// Do whatever you needed to do with the code here.
});
Live Example http://jsfiddle.net/VSrTg/2/
Edit An approach would be something like this:
$("#textarea").bind('paste', function(e){
var oldText = this.value;
setTimeout(function() {
// Compare oldText to $("#textarea").val() and format accordingly.
}, 1000);
});
​Edit 2 Given your revisions to your original post, if you're worried about the giant market share that is Opera, you're going to have to monitor the value of your textbox with a setInterval() and compare it against itself for changes.
Ultimately there will always be a way around your script, even the above example is susceptible to simply dragging text from another text box (or the address bar) into it without triggering the paste event defined above.

I would like to point out DOJO menu widget that is creating context menus perfectly in different browsers. http://www.dojotoolkit.org/reference-guide/dijit/Menu.html#dijit-menu
What you can do is that detect paste event in browsers that are supporting it and override context menu in browsers that are not supporting this event like opera.
Once you create your own context menu then you can add copy paste menu item or create context menu similar to the default using css.
Edited
Some browsers might not allow us to fetch clipboard content, in this case we can always revert back to flash for borrowing some of its features that are cross browser. See couple of links I posted in comments.
Its complete implementation might have more issues than anticipated but it is possible and we can always give it a try (I will for sure).

The answer to the question is a simple no. The main browsers that have no paste event are recent versions of Opera and Firefox 2. Given that there is no paste event, you need to find an alternative event or set of events to detect a paste from the context menu as it actually happens. You can add handlers for every event there is (I've done this) and you simply get nothing in the relevant browsers when a paste is triggered from the context menu by the user.
This only leaves polling the text input's value regularly, which is not the same thing. You could keep track of keypresses and observe in your polling code that the text input's value has changed by some means other than keyboard input and do a diff, but that's hacky and unreliable.

I use the setTimeout for paste events. But for context menu select nothing seems to work(as stated above). I bind a mousemove to the input's form which fires the update function. Then unbind/bind so they don't stack up.
This handles the context menu select and dragging value to input field.
If your form is small, say with only one input field and the mouse will not land on it after selecting from context menu, bind to the form's parent or document. Sure, it has to wait until the mouse moves but that is the general user action after selecting from context menu.
Works fine.