I think there is a problem with notifications.
with my account, they never disapear!

Exemple:
I have a new notification from @adesh1414127033 replying to my bug thread. I
I click on it, it goes to the reply and the reply blink, but the notification is still there ...

That is intended.

The notification color changes marking it as read when you click on it.

The behavior is same as facebook.

That is intended.

ok, but why some notifications never disapear ? ( i'm sure to have followed the notfication link!)
is it possible to add a button in all notification, mark all as seen ?

Mark as seen wont delete them , they were never meant to be deleted.

If you see, notifications appear in different color after you visit them which is meant to denote that they are read/seen

But, if you want, it is possible to change the behavior to delete seen/read notifications.
May be we can give an option in the backend to choose between these two behaviors ?

I would also like to see that implimented, I only want to see new ones displayed.