Use shelljs

Currently there is quite a bit of code that is obnoxious because of `node.fs`. Instead, we might want to use [`shelljs`](https://github.com/shelljs/shelljs) and have a lot of this be handled by the operating system.

Start by locating the analyzer code that uses node.fs and review how those operations currently work. Check shelljs documentation and the existing analyzer workflow before deciding which filesystem operations should change. Done means the relevant node.fs usage is replaced without changing analyzer behavior, with tests or checks passing if the repository provides them.

Written by the indexing model from the issue text.