Use commander package to replace current implementation of CLI options

[CDeltakai]

Description

This PR integrates the commander package and uses it to implement CLI options. This PR will also implement additional CLI options for defining file matching patterns and shellcheck patterns

Issues Fixed

• Fixes Use commander package to more efficiently setup CLI options #15
• Fixes Create centralized linting system that can be applied to all MatrixAI repos, regardless of project-specific linting rules #7

Tasks

• 1. Integrate commander package and use it to replace current CLI options
• 2. Implement additional CLI options to allow for defining folder matching patterns for eslint and shellcheck arguments

Final checklist

• Domain specific tests
• Full tests
• Updated inline-comment documentation
• Lint fixed
• Squash and rebased
• Sanity check the final build