Refactor, Documentation, and Code Cleanup

[filipchristiansen]

This PR includes a combination of refactoring, documentation, and code cleanup tasks to improve the codebase's structure, readability, and maintainability. The changes include:

Refactoring:

• Simplified logic in the _should_exclude function in ingest_from_query.py.
• Reorganized clone.py by moving the clone_repo function to the top of the file, above helper functions.
• Prefixed helper functions with an underscore for clarity and convention.

Documentation:

• Added docstrings to functions in process_query.py and the logSliderToSize function in server_utils.py.
• Enhanced main.py with docstrings and additional comments for clarity.

Style:

• Moved the comment for the async_timeout function into its body for better placement.

Chores:

• Added markdownlint to pre-commit hooks for enforcing markdown standards and disabling the line-length rule.

Fixes:

• Updated README.md to remove inline HTML and add a top-level heading to comply with markdownlint rules.

Code Cleanup:

• Removed the unused normalize_pattern function from client.py.
• Improved type annotations across multiple modules.

These updates collectively improve the maintainability, readability, and consistency of the codebase, while also aligning with coding standards and best practices.

[cyclotruc]

Very good once again you're doing wonders to the codebase, thank you