Add documentation site (Sphinx / Read the Docs) and API reference

[Marei33]

Summary

Adds a complete documentation site for matchmaker, built with Sphinx and wired up
for Read the Docs, plus the supporting docstrings and naming/consistency cleanups
that the API reference surfaced.

Documentation

New Sphinx site under docs/ (Read the Docs config, conf.py, requirements):

• Home – overview of the framework and the 5-step pipeline, with workflow figure
• Installation – setup + what pytest -s actually does (runs the rigid example
  pipeline, downloads reference data, manual fallback)
• Quick Start – runnable end-to-end walkthrough with a complete registration
  config and a "try it on the example data" command
• Usage – the three ways to use matchmaker: Snakemake workflow, individual CLI
  scripts (option tables), and the Python API
• Configuration Reference – every field of the registration and transform configs
• Understanding the Outputs – the log_dir tree, per-stage QC plots, and how to
  judge whether a registration succeeded
• Example data – what data is provided and how the synthetic data is generated
• Troubleshooting – common failure modes and fixes
• API Reference – curated public API via autodoc (mock imports so it builds
  without the heavy/GPU deps)

Code changes supporting the docs

• Docstrings (NumPy style) added/fixed for the curated public functions and the
  pipeline-stage entry points.
• Naming consistency – pipeline-stage entry points are now uniformly run_*:
  • cpd_from_images → run_cpd (and the low-level run_cpd → cpd_from_pcds)
  • match_points → run_matching
  • elastix_deformable_pointset_alignment → run_pointset_registration
    (and the low-level run_pointset_registration → elastix_pointset_registration)
  • run_registration → elastix_registration

Config / behaviour changes to note when reviewing

• output_name removed. The output .n5 name is now the optional
  fixed_image.name / moving_image.name (defaults fixed_image / moving_image).
  registration.smk, the example configs, and tests/test_pipeline.py are updated
  accordingly.
• Transform config fixed_image is now genuinely optional – apply_transform.smk
  guards it, so the overlay is simply skipped when it's absent.
• Bug fix: apply_transform.py used from utils import … (only worked in script
  mode); changed to from matchmaker.utils import ….

Previewing the docs

python -m venv /tmp/docs-venv && /tmp/docs-venv/bin/pip install -r docs/requirements.txt
/tmp/docs-venv/bin/sphinx-build -b html docs/source docs/build/html
open docs/build/html/index.html

Builds cleanly with no warnings.

Follow-ups (not in this PR)

• No LICENSE / CITATION.cff / CONTRIBUTING.md yet.
• README still needs to be updated/linked to the docs?

[Marei33]

WIP; needs to be updated when all open PRs are merged