> No warnings or communication of the exception were given. All trust I had in Flatpak was eroded from that moment on

This is just wrong. Clients like the flathub website or gnome software show the risk posed by wide ranging access to local files, but Flatpak has to support legacy applications that don't use portals yet and thus they can't block applications having those permissions

https://flathub.org/en-GB/apps/com.calibre_ebook.calibre

> calibre is potentially unsafe

> Full file system read/write access

> Can read and write all data on the file system