CLI improvements

The current CLI implementation is difficult to modify and it isn't particularly clear how different commands are structured. Adding a CLI command requires adding code in a bunch of places that all have to agree, and the same is true for options.

Improving this to work something like [CLI11](https://github.com/CLIUtils/CLI11) would be really cool, mostly in the sense of the ease of adding commands/options. Definitely doesn't need to be as extensive, but something simpler to use than what we have now would be great.

Also, should be turned into a C++ class to make the CLI easier to use in general.