This adds more logging in certain places, and adds logging to the CLI.
It also allows for certain commands in the CLI to be used without a
daemon connection, namely `init`, which previously required the daemon
to be connected, but now does not since it doesnt need it.
This commit massively overhauls the project's structure to simplify
development. Most parts are now correctly compartmentalized and
dependencies are passed in a sane way rather than global variables
galore xd.
