Both items surfaced by the 2026-05-07 arborist-vs-donto comparison
report (/home/fox/Downloads/arborist_vs_donto.pdf).
Ticket #000022 — adapter LossReport (PRD I9 analogue). Today wikitext
to_base() and html_page _normalize_text drop <ref> tags, image/category
wikilinks, HTML chrome, whitespace runs without recording any of it;
only the canonicalization-version pin survives. Ticket proposes a
sidecar adapter_loss_reports table (Option A) over Merkle-bound
loss_root (B) or audit-chain entries (C), preserving arborist's
"soft signals are sidecars" discipline. ~1.6% storage tax expected,
matching concept_relations. Doc-only; no code in this commit.
Federation doc-discoverability: PDF author concluded "federation
exists in code but the public docs page returned 404" because the
mesh page lives at /api/mesh.html and the concepts orientation
never surfaces the topic. Adds a "Federation across peers" section
to concepts.rst pointing at api/mesh, a :ref:\`federation\` anchor
+ context lead on api/mesh.rst, and a footer link in concepts.rst's
"Where to go next." Sphinx build passes; api/mesh.html#federation
deep link resolves.
Per shared-things convention: prefer 'our' for community-owned things;
'the' implies fixed singular ownership. The permacomputer is collective
infrastructure, so 'our' fits better than 'the'.
Updated three places (single canonical preamble text):
- LICENSE (Permacomputer Preamble section, our text — not the AGPL)
- README.md License section
- docs/_source/conf.py rst_epilog (per-page footer on RTD)
Previous attempt to move the full project TOC to the right via
html_sidebars={'**': []} stripped the theme's left sidebar — the right
sidebar in sphinx-book-theme renders only page-local TOC, not the
project tree, so the project structure disappeared and the page
looked unthemed.
Restore the default layout:
- Left: full project toctree (themed sphinx-book-theme sidebar)
- Right: 'On this page' (current page sections), expanded to depth 3
If we want a unified right-side project TOC later, that needs
pydata-sphinx-theme + secondary_sidebar_items override, not just
hiding the left.
sphinx_rtd_theme only renders left-side navigation. Switch to
sphinx-book-theme which puts the full project TOC on the right and
leaves the reading area centered.
conf.py:
- html_theme = 'sphinx_book_theme'
- html_sidebars = {'**': []} hides the left sidebar so the right TOC
is the single navigation surface
- show_toc_level=3 expands subpages; show_navbar_depth=2 controls top nav
requirements.txt: sphinx-rtd-theme → sphinx-book-theme>=1.1
Makefile cuts (64 → 58 documented targets):
- ingest-cur-parallel, ingest-old-parallel: parallel-shared mode
superseded by attached (no WAL contention)
- distill-shards: sequential never preferred over parallel variant
- bench-qa-quick: bench-qa-smoke covers same use case (~30s vs ~10s)
- ingest-grok, ingest-grok-media: single-DB grok rare; -attached is
canonical path
All cuts land in code that the underlying CLI still exposes — operators
who need the dropped variant call '.venv/bin/aborist ingest --shard ...'
directly. No behavior loss, just shortcut removal.
Docs improvements:
- New Concepts page (docs/_source/concepts.rst): orientation on what
aborist is, three layers (surface/core/providence), Merkle commitment,
8-dim cache key, audit chain, trichotomy + four-rung ladder, layered
verifier, falsification state, sidecars. Embeds module-graph and
verifier-ladder SVG diagrams.
- New Cookbook page (docs/_source/cookbook.rst): 8 recipes — recrawl,
falsify, ingest-self-providence, mixed-corpus query, LLM endpoint
override, integrity after bulk ops, bench, retrieval tuning.
- Quickstart embeds query-pipeline SVG diagram.
- docs/_source/diagrams symlinks to docs/diagrams so Sphinx can include
the SVGs (was orphaned, only README referenced them).
Better Makefile RTD page (docs/_source/_ext/makefile_targets.py):
- Group by workflow phase (Setup → Fetch → Ingest → Distill → Query →
Verify → Operations → Tests → Docs → Clean) instead of alphabetical
prefix. Tells a new operator the order they'd actually run things.
- Phase descriptions added; targets prefixed with 'make ' for copy-paste.
- Uncategorized leftover surfaces missing entries in PHASES list.
New docs/_source/quickstart.rst — install, two end-to-end paths
(Wikipedia 2003 + crawler), after-the-answer commands, query pipeline
overview, and links to deeper reference pages. Mirrors the README's
quickstart but adapts cross-references to the Sphinx structure.
Added to index.rst as a 'Getting started' toctree section above the
API modules — RTD users land on it first.
Use the canonical Read the Docs theme. Build dropped from 33 warnings
to 3 (most furo warnings were sidebar template lookups in the dark/light
mode switcher).
requirements.txt updated to pull sphinx-rtd-theme instead of furo.
- docs/_source/license.rst — new RTD page that literalincludes the
repo's LICENSE file (single source of truth, no duplication)
- conf.py rst_epilog — appended to every RST source so every doc page
carries the Permacomputer Preamble + AGPL-3.0-only notice + link to
the full license
- index.rst — adds 'Project / License' section to the toctree
The LICENSE file already had the full Permacomputer Preamble + complete
GNU Affero GPL v3 text (matches the whitepaper version).
Adds a Sphinx extension at docs/_source/_ext/makefile_targets.py that
parses the project Makefile's '## description' annotations and writes
docs/_source/api/makefile.rst at build time. Same convention 'make help'
uses, so the reference stays in sync with the source.
Generated page is grouped by target prefix (fetch-, ingest-, distill-,
docs-, etc.) and rendered as a list-table. Shows on RTD alongside the
autodoc API modules.
Generated file is gitignored — RTD regenerates on every build.
Initial docstring pass focused on syntax/style; this pass verified each
docstring against actual function behavior. Found and corrected:
WRONG (claimed behavior didn't match):
- _cmd_verify: claimed Q&A/audit verification — actually round-trips
Merkle proofs on N random documents
- _cmd_snapshot_verify: claimed Merkle proof round-trip — actually
re-derives snapshot root and checks for drift
- _cmd_evict: claimed 'archive unused content' — actually NULLs content
and removes FTS row; cores never evict
- _cmd_stats: listed 'index size' which is not in stats() output
OVERSTATEMENT (claim stronger than contract):
- _cmd_ask: 'grounded answer' — verifier may return UNGROUNDED
- _cmd_snapshot_list: 'named' — snapshots have hash roots, not names
MISSING IMPORTANT BEHAVIOR:
- _cmd_rehydrate: didn't mention drift-detection exit code
- _cmd_mesh_status: didn't mention 'enabled' flag (most important field)
- _cmd_distill: didn't mention recursive core→core distillation
- MerkleTree.proof(): didn't mention IndexError on out-of-range
VAGUE:
- _cmd_search: 'Search the corpus with FTS5' → mention output formats
Sphinx rebuild successful (29 warnings, down from 31).
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.
