That's the goal. "Web apps" are always going to be 2nd class apps, because it is insanity to allow the spoofing of the native UI. The security sandbox will always have significant restrictions, by definition. If you don't like this, write a native app instead.
> Reading/writing arbitrary files to the file system.
Are you trying to open up a massive security hole? Filesystem access is banned on purpose. Writing an extension in a way that guarantees arbitrary filesystem access cannot be exploited through some complex interaction with the rest of the browser environment is probably impossible (see: the Halting Problem). It would certainly fail in practice.
Seriously, stop treating the browser as the OS+desktop. If your platform doesn't offer any true "native" access that has the features you want, then take that up with the platform's vendor.