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This was done to allow greatly granularity when deciding what functionality is built into each board's build. For example, this way pulseio can be omitted to allow for something else such as touchio.
Adafruit's MicroPython Documentation
The latest documentation can be found at: http://adafruit-micropython.readthedocs.io/en/latest/
The documentation you see there is generated from the files in the whole tree: https://github.com/adafruit/micropython/tree/master
Building the documentation locally
If you're making changes to the documentation, you should build the documentation locally so that you can preview your changes.
Install Sphinx, and optionally (for the RTD-styling), sphinx_rtd_theme, preferably in a virtualenv:
pip install sphinx
pip install sphinx_rtd_theme
In micropython/, build the docs:
sphinx-build -v -b html . _build/html
You'll find the index page at micropython/docs/_build/html/index.html.