Improve error flow catching in code

[aaronjridley]

Description

Addresses #70 and #97

In making tests and running the code with different configurations, it is clear that the code needs more error catching and reporting. These changes use the report.error functionality and adds more capturing of possible user errors in trying to run the code.

This is not complete, since there are a million ways that the user can mess up running the code, but it adds a lot of catches in that should help. This is a constant process of adding more hooks.

Type of change

Please delete options that are not relevant.

• Bug fix (non-breaking change that fixes an issue) - capturing (more) bugs/issues in the aether.json file / settings
• New feature (non-breaking change that adds functionality) - I am slowly switching everything over to a model of setting an error in the report.error system and returning a didWork boolean of false, instead of trying to develop an iError integer flag that needs to be modified and added to. The report.error system is great for this.

How Has This Been Tested?

Hopefully, if the user messes up the aether.json file or some other file or makes a bad setting somewhere, the code captures this and reports it. There are no formal tests for this (except for the chemistry test).

Test configuration

• Operating system: Ubuntu
• Compiler, version number: gcc version 11.
• Any details about your local setup that are relevant: WSL and native Ubuntu

Checklist:

• [N/A] Make sure you are merging into the develop (not master) branch
• My code follows the style guidelines of this project
• I have performed a self-review of my own code
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation
• My changes generate no new warnings
• I have added tests that prove my fix is effective or that my feature works
• New and existing unit tests pass locally with my changes
• Any dependent changes have been merged and published in downstream modules
• [N/A] Add a note to CHANGELOG.md, summarizing the changes