Fixes for initial app setup

[Alonkad]

Description

This PR fixes multiple issues with initial setup of the app:

• MongoDB deprecation warnings
• Node deprecation warning
• createBrowserHistory deprecation warning
• Adding .env file to .gitignore
• Fixing error with HMR (I went with this fix)
• Change frontend port to 3001 as 3000 is taken by backend server

Please review this PR commit by commit (except for the last 2 commit for fixing yarn.lock files)

Type of change

Please delete options that are not relevant.

• Bug fix

How Has This Been Tested?

Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce. Please also list any relevant details for your test configuration

• Run ./start.sh - see all deprecation warnings gone in the terminal
• Run ./start.sh - see deprecation warning gone browser console

Checklist:

• I have performed a self-review of my own code
• I have made corresponding changes to the documentation
• My changes generate no new warnings
• I added the relevant people as reviewers to my PR

[vanessa-cooper]

It looks like we still have some problems.
To make it easier for new engineers to get the system up and running, is there a way you can make the readme file a bit more friendly?