Migrate documentation to Read the Docs

[harryswift01]

Summary

This PR migrates the main prepmd documentation from the repository README.md into a structured Sphinx documentation site suitable for Read the Docs.

The README is kept as a shorter project overview, while the detailed installation, usage, API, and developer documentation now live under the new docs/ structure.

Changes

Add Read the Docs/Sphinx documentation structure:

• Added a docs/ directory generated using Sphinx.
• Added the main documentation index and separate documentation pages.
• Added .readthedocs.yaml to configure Read the Docs builds.
• Added Sphinx build files for local documentation generation.

Move README content into documentation pages:

• Moved detailed usage information out of README.md.
• Added structured pages for installation, quickstart, Python API usage, running with runmd, developer notes, and future work.
• Kept the README focused on a shorter overview of the project.

Add API documentation support:

• Added Sphinx autodoc/autosummary configuration.
• Generated initial API documentation pages for the prepmd package.
• Added optional dependency mocks for autodoc so the documentation can build without requiring all runtime dependencies.
• Configured the documentation to use the furo theme and copy-button support.

Impact

• Makes the documentation easier to navigate and maintain.
• Aligns prepmd with a standard Read the Docs documentation workflow.
• Provides a clearer split between the README and full user/developer documentation.
• Enables future versioned documentation through Read the Docs.
• Documentation builds successfully with Sphinx, although some existing docstrings still produce formatting warnings that can be cleaned up in a follow-up PR.