But...why? Why would I ever need to interact with any of the application files? Why would I need to move it to another portion of the disk? Give it a shortcut to click on to activate it and who cares? It could be running one file or a million files. The only files I care about are the ones I create and edit. I can't imagine any need to interact with the application files. If your users need to interact with the application files or move them around in any way, you've already failed at usability.
The way the Mac handles it, is a great way. An application is a directory with a special structure. The finder treats that directory like a file. You can double click it for launching the application, you can move it like a single files. Usually, no installation is required. That also means, deinstallation is a single delete. On the shell you can just cd into that directory like any other.
This way, the application developer does get all the benefits of a file system, while the user all of having a single file. While you don't need to do this constantly, being able to relocate an application on your file system is a very nice thing. Like moving it to a different volume or disk. Having it an a users home or the system application directory. Especially, having any amount of compies of the application (different versions) in as many places as you want.
Not having the need to "install" an application is a big advantage, not having to "deinstall" an even bigger. Having the application doesn't change your system. This is especially great if you run your systems for many years. Having to do a "clean install" is a symptom of a not cleanly separated system.
> Why would I need to move it to another portion of the disk?
Sometimes you want to store applications on different disks. Like say a removable USB drive so you can use it at multiple computers, or you want to run some from an SSD but others are ok running from a larger slower disk. Or maybe you just want to run them directly off the network. "Installation" is just a copy operation from one media to another, "uninstallation" is just a delete operation. In other words: there is a minimum of abstraction, the application is a single file and performing the same operations you do on any other file to them does exactly what you think it does and the application is stored exactly where you think it is stored.
The author mentioned "the Haiku operating system each application is one package, and each package is one file that is loop-mounted into the filesystem to make its contents accessible."
Now if you don't ever need to interact with application files why invent all this complexity when you can just expose the files individually and not ever care about that again.
Maybe it's easier for development if they're individual? Who knows? As a user the number of files needed for an application is irrelevant. Maybe the dictionary that Word uses for the spellchecker doesn't need to be a part of the executable, so if they want to update it, they can replace just that file and they don't have to make you download the entire program again?
But...why? Why would I ever need to interact with any of the application files? Why would I need to move it to another portion of the disk? Give it a shortcut to click on to activate it and who cares? It could be running one file or a million files. The only files I care about are the ones I create and edit. I can't imagine any need to interact with the application files. If your users need to interact with the application files or move them around in any way, you've already failed at usability.