Move shell out commands into separate library

[Pierre-siddall]

PR Summary

Code Reviewer: @ericaneininger

This PR aims to unify shell out commands across MOCI so that they all have the same semantics. The changes involved include adding a separate library to handle shell operations and replacing current shell operations with a newly implemented exec_subprocess function.

closes #12

Code Quality Checklist

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Testing

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  tests, unit tests, etc.)

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