Refactoring Commands

Now that we have the `commands` package set up, it's time to move everything over to it. This PR is currently not ready for merge, just setting it up for CR.

The basic scope of this PR is as follows:
* Set up transports based on `commands` package (HTTP RPC server/client, CLI command handling)
* Refactor existing commands for the new API (won't be a 1:1 mapping, commands will change)
* Make changes to `commands` package when necessary
You only want to `parseArgs`, etc _after_ you've chosen the root. so just add a `chosenRoot` variable to keep track of the one.