refactor(filesystem): prefer our fs wrapper to node's fs

[Hweinstock]

Problem

In some places we need node's fs due to sync behavior or unsupported functionality. In all cases where we don't strictly need it, we should be using our fs wrapper.

Solution

• Replace as many uses of node's fs with our fs as possible. (Avoiding major refactors)
• Ban import fs (via eslint), and allow for exceptions.

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License: I confirm that my contribution is made under the terms of the Apache 2.0 license.