apply: Provide more context when failing to clone the repository

As I was touching code around this, let's take the opportunity to propagate the
error back to a RunE cobra function. This commit touches a few commands but
that was the minimal set of changes when touching pkg/manifests.

Style fixes

although this isn't my personal preference, it appears that this method (which is predominantly used elsewhere in the project anyway) is considered the most portable.

refactor: extract `addon *` and `registry-sync-commands` commands to separate packages

This seemingly introduces duplication, but IMO this constant is a style implementation detail that doesn't make much sense to share between different places.
Column-based pretty-printing looks depend on the exact data being shown. If we think that it's the same data being printed in both places, then we should extract & share a bigger chunk of code than just one const.

refactor: Split out `apply` and `plan view` into subpackages.

PersistentFlags() makes subcommands inherit these flags. This is not necessary in this situation, so I'm simplifying it.

This is because we don't seem to use the context in any meaningful way here.

Refactor: extract `specs` from `main` to a separate package.

This change is intended to clean up the code, but leave behavior unmodified.