Set default permissions in `metadata.Manager` to 0644
Currently all files and folders created with the `metadata.Manager` (which is the core FS management subsystem) are created with permissions 0777, i.e., everyone has all permissions. This commit transistions us to a more locked down permissions set, 0644, which allows the user to do everything except execute, and everyone else to only read. Since we don't store any app code that needs to be executed, this should be suitable for everything. Fixes #136.
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