I doubt the brain is telling the fingers to spread to an absolute unit of length, but rather relative to some object. In both cases, just large enough to grasp the circular object, however large it might be.

I know the point he's making; I read the blog post. I don't know why you assume I didn't. I'm saying that I believe it is unrealistic to expect that a user will not attempt to interact with a notification on the screen if it's there. More than likely they will be entirely confused when the mouse goes "under" the notification, which is unlike anything else on the system.

His point is that the ability to interact with notifications means that you have to decide, in the two or three seconds that the notification is on-screen, whether or not you want to interact with it. That's distracting, which makes notifications annoying.

You don't have to decide anything, actually. You can read it or not. Having the ability to interact with the notification doesn't change anything about the interaction with the notifications up until the point the user decides to interact with it, which I believe the user will do initially anyway regardless of whether he can actually interact with it or not.

Personally, I'm with him. I hate it when I try to switch desktops, close a window, open my IM client, or whatever, and a notification pops up to block my click (or catch it and do something unexpected).

This is a valid concern that can be addressed in other ways, but I don't think the way highlighted in the article is a good one because, again, users will not expect that their mouse will go under the notification. I guarantee a non-insignificant number will sit and wait for the notification to go away before clicking on something they want underneath. This is indicative of an interface that is not as intuitive as it could be.

Huh? It sounds nothing like that. If you want to draw a comparison, it looks and sounds a lot like Growl notifications on OS X.

What I meant to say was, "increase opacity."

Having the notification bubbles disappear when you mouse over (well, under) them doesn't seem usable. The user will see the bubble and want to interact with it in some way. Mousing over should decrease opacity and allow the user to interact with the dialog, such as immediately remove it or click on it to bring up the application that spawned the notification. I'm very familiar with computers, and it still seems very strange to "mouse under" something.

There are already a few solutions for bug tracking in a git repository (here is one example that also includes a minimalist web interface), though from what I've seen nothing really compares to hosted solutions as of yet. It's great for simple projects, though, especially when you're just starting out and want to keep track of todo items and such.