These limitations are all slowly disappearing as web standards are advancing fast to fill these gaps. I think soon we'll be able to give trusted web apps permission to read/write to our file systems and reach out to more OS-level interfaces that our browsers have access to.
Web apps also offer advantages over native apps, like zero installation, universal compatibility regardless of OS, and the ability for publishers to put updates/patches out instantly.
This sounds like something perhaps the dropbox api would be useful for? The webapp would simply modify files in your dropbox through the api, and changes could then be pushed to your local machine through dropbox's service.
Making changes to the code to bring support to new "OS's" in this case is easy as long we're talking about the webkit gang + Firefox, which makes up most users who will have interest in webapps.
Web apps also offer advantages over native apps, like zero installation, universal compatibility regardless of OS, and the ability for publishers to put updates/patches out instantly.