If you know the right identifiers, you should be able to use WebUSB to access a flash drive/external hard drive. Combined with C-to-WASM compilers and Linux driver code, I'm sure you can defragment from the browser alone.
Or you can hook this mechanism into one of the WASM x64 emulators and attach the drive directly to a copy of MS-DOS or Windows 98 running in the browser.
Why do APIs like this even exist? There's no legitimate reason for an HTML webpage to need this, it's just creating more attack surface for bad actors.
The File System API is a JavaScript API, not an HTML one, so it helps to think about it from that light (programs, not documents). The API allows tools such as photo editors, file converters, code editors, and the like to be given access to a set of files they can work on directly rather than needing to import and export from the browser on every change. If the attack surface is too much for a use case it can be globally denied by default in every major browser so you won't even get prompted.
The page needs permission. That permission step is similar to the act of downloading a native app. Except for the fact that the broswer gives even less access to your system
than a native app so it's safer than a native app. (at least on desktop) That file system API is super useful for cloud based IDEs as just one example
Or you can hook this mechanism into one of the WASM x64 emulators and attach the drive directly to a copy of MS-DOS or Windows 98 running in the browser.