Added API Docs

[srivarra]

Added and reformatted documentation for functions across biahub.

This required some of the following changes as well:

• Updated type hints and docstrings across the codebase:
  • Migrated Python type hints with (PEP 585): List → list, Optional[X] → X | None, etc.
  • Standardized docstrings to Numpydoc format with Parameters and Returns sections.
• Using the root contributing.md file instead of copying the one in the docs directory.

Note: We should add Ruff rules for docstring validation in a separate PR. But that can happen after a larger Ruff (with minimal rule selections) + uv PR.