Store read-only permissions

## Overview

Vorpal has been slowly adopting reproducibility practices where it can and will eventually need to support making sure all files in the store are properly set to read-only WITHOUT breaking any other permissions that may exist (exec, etc).

## Changes

This will require going into the source code and finding all places files are placed in the store and properly set them to read only. This should be separate from the already existing "set_timestamps" function as that has value outside of setting permissions.