Make repo branch configurable

## Overview

We want to add an option to the CLI to allow for users to override the branch of their local repo when retrieving files or generating reports based on file content.

## Requirements

- branch should be optional
- `--branch`
- defaults to `master`

## Approach

TBD

## Security and Privacy

N/A

## Test Plan

- Unit tests and integration tests

Start at the CLI entry point and trace how the local repository branch is selected when retrieving files or generating reports. Add the optional --branch setting with master as its default, then verify the behavior with unit and integration tests, including an explicitly supplied branch.

Written by the indexing model from the issue text.