Refactor how CLI commands are added to `pepr` in `src/cli.ts`

[samayer12]

Describe what should be investigated or refactored

While working on #2395, I noticed a pattern in Pepr that seemed a little counter to how commander composes commands and subcommands.

We should add commands to the root pepr command by using .addCommand() instead of our current approach of passing the entire pepr command object into a function that adds on another subcommand. The outcome will be the same, but the way we modify the CLI structure should be more intuitive to someone unfamiliar with the project.

Links to any relevant code

src/cli.ts

Our current approach is something like:

import subcommand from "somewhere"
const program = new Command()
subcommand(program)

A preferred approach modeled in #2395 would be like:

import subcommand from "somewhere"
const program = new Command()
program.addCommand(subcommand)

Additional context

Commander docs