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IN-906 Include creation of SQLAlchemy engine in main workflow

Why these changes are being introduced:
* This change contributes to improved code readability and cohesion as it
results in all method calls being executed through the CLI's main function.

How this addresses that need:
* Removing engine creation from db.py
* Creating an instance of DatabaseEngine in cli.py
* Adding the engine as a parameter to classes and methods in app.py
* Update tests

Side effects of this change:
* None

Relevant ticket(s):
* https://mitlibraries.atlassian.net/browse/IN-906

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