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Background: Somehow the security permissions on many folders in ProgramData got changed to allow access only to my user account. This caused a variety of problems such as services not starting because the SYSTEM user couldn't access files. Using icacls and lots of googling I restored full access to SYSTEM and Administrators and read/execute access to Users, but there will still problems. Metro Apps (or whatever we are supposed to call them in Windows 10) were crashing immediately after opening. More googling revealed that I needed to add permissions for the "ALL APPLICATION PACKAGES" user. Now everything seems to be running okay, but I am left wondering what other permissions are still missing, waiting to cause problems in the future.
Question: Is there a way to restore the full set of necessary default permissions to system folders like ProgramData and Windows?
I can't help with your problem but I really like the way you've formatted this question, with the clearly labelled "Background" and "Question" sections. There are so many questions where you're reading a long set-up and thinking, "Blah, blah, blah but what's your question?" and you've forgotten half the background by the time you find out what the question is. This format makes it really easy: skip ahead to the question, so you know where things are going; read the background so you know what the problem is; read the question again and (if possible) answer it! – David Richerby – 2015-08-08T14:08:52.503