Rename duplicated System.Permissions module

[snoyberg]

Both the pantry and stack packages had the same module name, which
prevented stack ghci from working. This rename resolves the problem.

Note: Documentation fixes for https://docs.haskellstack.org/en/stable/ should target the "stable" branch, not master.

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• Any changes that could be relevant to users have been recorded in the ChangeLog.md
• The documentation has been updated, if necessary.

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