I doubt many people will see this, but boosting is very much appreciated as I want to hear as many opinions as possible.
If you created your own file structure. would you have information relating to programs be separated by category and then app i.e.
State
App 1
App 2
Data
App 1
App 2
Sources
App 1
App 2
Binaries
App 1
App 2
(think like XDG base directories)
or separated by application, and then by category, i.e.
App 1
State
Data
Sources
Binaries
App 2
State
Data
Sources
Binaries