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
why is this modifying `req` at this point?? because we changed it to be JSON always? (why do we do that, wont the HTTP api be able to handle different encodings? 

in any case, flag this with a comment as to why its here.