What does any of this have to do with a GUI? And for transporting, extract the data into a portable bundle, or take the entire store.
> Is the application store the only way to start at app? If I bind a global hotkey to start an app how is that handled?
Again, what does any of this have to do with how the applications are stored? Can you see the files that make up an iOS app? You can still start them, can’t you? A macOS app is a folder called Something.app, the actual binary lies somewhere inside. Do you typically need to poke inside the .app folder?
> How about I have an addon for firefox that allows me to bind keys to operations which can include javascript which can itself start applications which can then write to files.
As far as the computer is concerned, you are merely starting a process. Again, what does that have to do with how applications are stored. They can be triggered however and wherever they are stored.
> Do I have to access my photos via a a singular photo manager? I can imagine images accessed in 17 different contexts by 30 different apps does each of them need permission to access each dir which contains images or just generically to access images
This is already being handled on iOS and Android. Photos apps is merely the default interface for the PhotoStore. You can access your photos from any app.
> Does this mean that a singular permission would control both access to the browsers cached image of the ycombinator logo on this page and some ones nude selfies?
Namespaces inside individual stores, or separate stores.