There is a transition from a file-centric to an app-centric model, that I mostly disapprove of, but that's what is happening. Before, you had files stored in a filesystem, you picked the file and opened it with the app. On Windows, you double-click on the file, on a command line, you type "app filename". Now the trend is to first open the app and then use the app to fetch your data, that data is entirely managed by the app and may be stored in an opaque area of a filesystem, some server on the internet, etc...

I disapprove of the "new" way (that is not so new, but it is the current trend) because it favors lock-in and general loss of control. But there are also some advantages such as being able to do versioning, syncing, collaborative work, searching and general database-like operations when your filesystem doesn't support it. A lot of popular open source "not evil" software use that model, for example, IIRC, Firefox has always stored bookmarks in an opaque sqlite database while Internet Explorer stored them as files in a folder, and I don't think I need to tell you which one is considered the most evil.