How can i make an app that will work for desktop windows and IOS with phonegap?

I want to be able to access folders and files via my app, the problem is, when i want to access files on the desktop, i have to run it from a server or at least to emulate one using a program like xampp. I know PhoneGap has it's own API to access files, but i need to make the app work on desktop too, and i don't mind it to be as normal offline website ( via index.html, not an exe ), but i still need to solve the security issues, i can't tell clients to run it from a server...

The big idea after it, is that i need the app to check for new files in the server, if there are any, to download them. Also, i want the app to be able to access those downloaded files when it is offline as well.

I guess using only phonegap in ios will solve this, but i still need it to work on windows desktop as well.