Improve Getting Started documentation clarity and workflow

[harryswift01]

Summary

This PR improves the clarity and usability of the CodeEntropy documentation and performs light cleanup of unused command-line arguments. The changes focus on making the Getting Started workflow easier for new users, while removing deprecated or unused CLI flags and improving cross-referencing within the developer documentation.

Changes

Improve Getting Started documentation

• Reordered examples so the smallest, fastest-running example appears first.
• Paired each example’s config.yaml with its corresponding CLI command.
• Added estimated runtimes to help users select appropriate examples.
• Explicitly documented the required working directory and clarified where output files are generated.

Remove unused CLI arguments

• Removed deprecated or unused flags from arg_config_manager.py.
• Simplified the available argument set to better reflect current functionality.
• Reduced potential confusion caused by obsolete options.

Improve developer documentation

• Added references to the contributing guidelines within the developer guide.
• Improved navigation between developer-focused documentation pages.

Impact

• Makes the Getting Started guide easier to follow for new users.
• Reduces setup friction and common errors related to execution context and output location.
• Simplifies the CLI, improving maintainability.
• Improves discoverability of contribution guidelines for developers.

[jimboid]

Thanks for doing this. Some valuable changes to the documentation including purging old dangling features and improving the getting started docs for new users. A great PR!