Fix ReadTheDocs build: Import README.md and enable CLI documentation generation

[Copilot]

ReadTheDocs was configured to include README.rst (doesn't exist) and CLI documentation failed to generate due to __file__ being undefined in Sphinx import context.

Changes

Markdown Support

• Added myst-parser extension to docs/conf.py and docs/requirements.txt
• Updated docs/index.rst to include README.md instead of README.rst

API Documentation Fix

Fixed snakedwi/run.py to handle Sphinx import where __file__ is undefined:

# For Sphinx doc generation, __file__ may not be defined
try:
    app_path = Path(__file__).resolve().parent
except NameError:
    # Fallback for Sphinx - use snakedwi module path
    import snakedwi
    app_path = Path(snakedwi.__file__).parent

Configuration

• Created .readthedocs.yml with Python 3.12 and proper build settings
• Updated snakebids version in docs requirements from ==0.2.1 to >=0.14.0,<0.15
• Added docs/_build/ to .gitignore

Result

Documentation now builds successfully with README content on index page and full CLI argument documentation.

Index page with README.md:

CLI API documentation:

Original prompt

update the docs, which use readthedocs, importing the README.md as the title page, and making sure the other api pages are generated properly

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