Clean module naming: numpy_impl/ + topic names (#34)

[neuromechanist]

Closes #34 (epic delivered as a single PR per maintainer decision).

Drops the amica_/pyAMICA/_torch_ng module-name sprawl for topic-based names. Pure structural rename — no behavior change.

Changes

• NumPy reference → pyAMICA/numpy_impl/: pyAMICA.py→core.py, amica_newton.py→newton.py, amica_pdf.py→pdf.py, amica_data.py→data.py, amica_load.py→load.py, amica_viz.py→viz.py, amica_utils.py→utils.py, amica_cli.py→cli.py; new numpy_impl/__init__.py exposes AMICA. params.json moved alongside its loader (numpy_impl/core.py).
• PyTorch: torch_impl/amica_torch_ng.py → torch_impl/core.py.
• Public import surface unchanged: from pyAMICA import AMICA, AMICA_NumPy, AMICATorchNG (plus the numpy_impl/torch_impl subpackages). No compat shims — every call site, test, the CLI entrypoint (python -m pyAMICA.numpy_impl.cli), and the live docs (AGENTS/README/MIGRATION/PROGRESS) were updated directly.
• Packaging fix (latent bug): pyproject.toml now lists the subpackages explicitly and ships numpy_impl/params.json as package-data. A bare packages=["pyAMICA"] dropped torch_impl/ (and params.json) from the built wheel on some setuptools versions, so a pip-installed import pyAMICA / AMICA_NumPy() would have failed; both now work from a clean wheel install.

Layout decision

numpy_impl/ subpackage (symmetric with torch_impl/), per maintainer choice.

Tests / verification

• pytest -m "not slow": 85 passed, 5 skipped, 1 xfailed (matches CI exactly). All moves preserved as git renames.
• Wheel builds and a clean-venv import pyAMICA + AMICA_NumPy() succeed (with numpy_impl + torch_impl + params.json present).
• Public API round-trips: AMICA_NumPy is numpy_impl.core.AMICA, AMICATorchNG is torch_impl.core.AMICATorchNG. ruff clean.
• .context/ ADRs and issue notes are archival (point-in-time records) and intentionally left referencing the old paths.

[neuromechanist]

Review response (code-reviewer, Sonnet)

No critical or important findings. The reviewer verified completeness by grep + built and installed the wheel, imported the public API from it, ran python -m pyAMICA.numpy_impl.cli end-to-end on real EEG, and confirmed 0 content changes beyond import-path rewrites.

• Fixed the one sub-80 nitpick: README's "File Structure" now lists numpy_impl/params.json (and adds torch_impl/core.py / numpy_impl/core.py) instead of a bare params.json.
• .context/scratch_history.md's old python -m pyAMICA.amica_cli line is left as-is — it's an archival debugging log, not runnable docs (consistent with leaving .context/ ADRs/issue notes untouched).