The Sandbox: Banning LaTeX From the Mac App Store
Texpad will parse the file, automatically open included files, and present them all to the user in a unified editor. […] This behaviour is ruled out by the Sandbox because the user has only granted permission for Texpad to open the root file itself. We would never do it, but we could avoid this limitation by wrecking the user experience, forcing the user to open the files one by one. Unsolvable however is the problem of LaTeX itself, which can never be compatible with the Sandbox.
Presumably, Apple expects such applications to prompt the user to authorize access to whole folder hierarchies, and then persist that via security-scoped bookmarks. They’re not dogfooding this approach with Xcode, iTunes, Aperture, etc., though. If every application started doing stuff like this it would become annoying and train users not to scrutinize such the dialogs very carefully.