docs: add Sphinx API reference generation from docstrings

Implements Read the Docs infrastructure to generate API documentation
directly from code docstrings. Replaces static modules.md (1200+ lines).

New structure:
- docs/_source/conf.py — Sphinx configuration (furo theme)
- docs/_source/index.rst — Main TOC
- docs/_source/api/*.rst — Module groups (substrate, storage, retrieval,
  qa, distill, mesh, cli)
- docs/_source/Makefile — Local build targets
- docs/_source/README.md — Documentation on building and extending

Makefile integration:
- make docs-api — generate HTML (output: docs/_source/_build/html/)
- make docs-api-clean — remove build artifacts

Build output (40 HTML files):
- API module reference with docstrings
- Source code links (:viewcode: extension)
- Full-text search index
- Module index (genindex, py-modindex)

Sphinx installed in venv as dev dependency. HTML is browseable at
docs/_source/_build/html/index.html (open in browser after build).

This justifies the deletion of modules.md: code docstrings + Sphinx
autodoc = automatically-generated, always-current API reference.

docs/_source/api/cli.rst

@@ -0,0 +1,8 @@
+CLI: Command-line interface
+============================
+
+Entry point for all aborist operations.
+
+.. automodule:: aborist.cli
+   :members:
+   :undoc-members:

docs/_source/api/distill.rst

@@ -0,0 +1,9 @@
+Distillation: surface → core compression
+==========================================
+
+Surface-to-core extraction and recursive distillation.
+
+.. automodule:: aborist.distill
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/_source/api/mesh.rst

@@ -0,0 +1,9 @@
+Federation: multiplayer aborist
+================================
+
+Gossip-based mesh for cross-peer data sharing.
+
+.. automodule:: aborist.mesh
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/_source/api/qa.rst

@@ -0,0 +1,67 @@
+Q&A Pipeline: question → answer → verify → cache
+==================================================
+
+Question answering, caching, verification, evidence mapping.
+
+keys
+----
+
+.. automodule:: aborist.qa.keys
+   :members:
+   :undoc-members:
+
+runner
+------
+
+.. automodule:: aborist.qa.runner
+   :members:
+   :undoc-members:
+
+query
+-----
+
+.. automodule:: aborist.qa.query
+   :members:
+   :undoc-members:
+
+verify
+------
+
+.. automodule:: aborist.qa.verify
+   :members:
+   :undoc-members:
+
+evidence
+--------
+
+.. automodule:: aborist.qa.evidence
+   :members:
+   :undoc-members:
+
+quantifier
+----------
+
+.. automodule:: aborist.qa.quantifier
+   :members:
+   :undoc-members:
+
+metacognition
+-------------
+
+.. automodule:: aborist.qa.metacognition
+   :members:
+   :undoc-members:
+
+dag
+---
+
+.. automodule:: aborist.qa.dag
+   :members:
+   :undoc-members:
+
+client
+------
+
+.. automodule:: aborist.qa.client
+   :members:
+   :undoc-members:

docs/_source/api/retrieval.rst

@@ -0,0 +1,35 @@
+Retrieval: FTS5 search and concepts
+===================================
+
+Full-text search, concept relations (synonym/rivalry overlay).
+
+search
+------
+
+.. automodule:: aborist.search
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+sources
+-------
+
+.. automodule:: aborist.source
+   :members:
+   :undoc-members:
+
+.. automodule:: aborist.sources.wikipedia
+   :members:
+   :undoc-members:
+
+.. automodule:: aborist.sources.html_page
+   :members:
+   :undoc-members:
+
+concepts
+--------
+
+.. automodule:: aborist.concepts
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/_source/api/storage.rst

@@ -0,0 +1,27 @@
+Storage: SQLite schema and audit
+================================
+
+v9.8 SQLite schema, audit chain, and cross-shard views.
+
+store
+-----
+
+.. automodule:: aborist.store
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+ingest
+------
+
+.. automodule:: aborist.ingest
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+evict
+-----
+
+.. automodule:: aborist.evict
+   :members:
+   :undoc-members:

docs/_source/api/substrate.rst

@@ -0,0 +1,27 @@
+Substrate: Core data structures
+===============================
+
+Pure Merkle tree and document primitives.
+
+merkle
+------
+
+.. automodule:: aborist.merkle
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+document
+--------
+
+.. automodule:: aborist.document
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+wikitext
+--------
+
+.. automodule:: aborist.wikitext
+   :members:
+   :undoc-members: