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The difference should not exist in theory. Both are programs running inside a computer, with the difference that the web application is a doomed version of the full runtime environment that the Operating System is able to really provide, for a reason: compatibility.

Imagine something like POSIX but much more extended, covering APIs for GUI, database access and so forth (basically what the Java VM provides), the "Application Browser" can just be an url in the form app://foobar.com/email.app that will run as native application. Still it can be a server-side application where all your data is saved server-side, and of course the environment can be smart enough to automatically download and install a new version of the program when available (actually the local copy can be just a caching business).

The web is going to offer all this in the end, but currently it's ridiculous stupid compared to a real environment. You can't do free networking, for instance, things like opening a socket and sending/receiving data using a non-HTTP protocol. In the end the web will provide all the stuff that now are trivially done in the desktop side, but my feeling is that this was the wrong path since everything is already here, the technology and decades of desktop applications capable of doing very smart things.

We are reinventing the wheel using the wrong foundation (HTML+CSS for GUIs, GET requests for all the kind of networking, ...).




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