Updates

Recent changes to the public research, software, citation, evidence, and discovery index.

2026-06-21

  • Added two Zenodo publications: **Template Madlib** (zenodo.20786638, ) — docxology/template_madlib, deterministic token injection for conditional IMRAD manuscripts — as work **172**, and **California Public Records** (zenodo.20789899, ) — a technical and legal reference for the post-AB 473 era — as work **173**. Downloaded both PDFs, generated work/paper pages, and registered papers/README.md entries. Bibliography **170→172**; paper folders **153→155**. Also added the previously-missing **COGANT-0.6.0.pdf** and removed a duplicate On-Policy Distillation folder.
  • Repo-wide **Zenodo DOI concept-consistency** pass: switched **70** bibliography rows (plus the 4 newest works and the itrace / ntqr_llm / on_policy_distillation software-catalog links) from per-version DOIs to their **concept DOIs**, each verified against the Zenodo API conceptdoi field so the citation always resolves to the latest version. Deliberately excluded version-distinct works that share a single concept DOI (e.g. the AII Ecosystem v1/v2/v3 snapshots) to avoid duplicate DOIs.
  • Added **AGEINT** (docxology/AGEINT) and **template_madlib** (docxology/template_madlib) to the software catalog: docxology owned **58→60**, Grand Total **92→94** (Education 5→6, Developer Tools 15→16); recomputed the GitHub-inventory curated split.
  • Fixes: sync_publications_html.py now patches twitter:image:alt with the live work count (was stale at 170); removed a doubled "Abstract" heading and added the MIT license field in the On-Policy Distillation paper folder; reconciled that folder's metadata to its concept DOI.

2026-06-17

  • Added **AGEINT: Agentic Intelligence** (zenodo.20732275, ) — docxology/AGEINT v0.1.0, a Synthetic Analytic Tradecraft curriculum-and-assurance atlas — as work **170** via the canonical sync_paired_publications.py apply path, scoped --since 2026-06-16 to isolate the single new release. Stripped the <p> HTML the Zenodo abstract carried into metadata.json/README.md; renumbered the papers/README.md index strictly **1..152** (closed the gap at 111 left by the CEREBRUM dedup, plus a duplicate 152). Regenerated all dependent surfaces. Bibliography **168→169**; paper folders **151→152**; software unchanged at **91**; Computational domain **27→28**. Identified **CEREBRUM** (zenodo.15231156) and **Self-Improvement Agent Harness** (zenodo.20693012) as re-versions of existing works …010 / …127 (newer version DOIs of already-curated concepts) — update-only, not new rows.

2026-06-15

  • Completed **COGANT** (zenodo.20705351, ) and **coasys** / **COGANT** software-catalog intake after commit b6fa1b4: added 2026_COGANT to papers/README.md (151 folders), paper_metadata.json, and the Computational domain blurb (27 works); regenerated publications, software, sitemap, resume, evidence, search, feed, domain, and count exports. Bibliography **167→168**; software catalog **89→91** (58 owned + 33 AII); paper folders **150→151**.

2026-06-14

  • Added two Zenodo-only publications via add_zenodo_only.py: **DemoCreate** (zenodo.20693217, ) and **ENTO** (zenodo.20647443, ); added the **GeneralizedNotationNotation (GNN)** software v2.0.0 (zenodo.20671741, ) as a distinct work from the 2023 GNN paper (different Zenodo concept). Bibliography **165→167**.
  • Completed the CEREBRUM dedup the 2026-06-10 pass flagged for the maintainer: removed the duplicate work …118 (papers/2025_CEREBRUM2, the v1.4 deposit zenodo.15231156) outright, keeping the primary …010 (papers/2025_CEREBRUM, zenodo.15170907). Retired the now-empty WORK_CANONICAL_OVERRIDES entry and its regression test; re-pointed the CEREBRUM software-catalog entry to the surviving paper folder. Removed-work numbers are retired, not renumbered, so existing work-page URLs stay stable — sync_publications_html.validate_rows now allows numbering gaps (strictly-increasing instead of exactly-sequential).
  • Re-pointed the template/ Reproducible Generative Research bibliography entry (row 1) to its latest release zenodo.20669283 (v3.4.0).
  • Reconciled all volatile-count surfaces to **167 works / 150 paper folders** (BIBLIOGRAPHY header + per-domain counts, papers/README, index.html, DISCOVERY, and the regenerated data/exports); count-consistency drift clean, 92 tests passing.
  • Hardened work identity without a URL migration (FirstPrinciples/RedTeam scoping concluded slug/DOI URLs would cost 168 forever-stubs on a no-redirect static host). build_work_pages.py now fails loud on a duplicate citation_key (was silent last-write-wins page overwrite); new test_frozen_work_keys.py freezes every num → citation_key so a retitle that would churn a live URL fails CI; documented works/{citation_key}.html as a permanent opaque contract in the canonical policy.
  • Modularized docs/ from 7 flat files into topic subdirectories (operations/, seo/, design/, security/, releases/) with a new docs/README.md navigation index; updated all inbound references across code, agent entrypoints, and the search index. docs/AGENTS.md retained as agent operational guidance.
  • Documentation/signpost accuracy pass: reconciled five hand-maintained narrative pages (LINKS, PROFILE, WIKIPEDIA, COLLABORATORS, MEDIA) that had silently drifted to 125/154-work counts → **167**, and added them to count_consistency so they can no longer rot. Linked the new docs/README.md index from README.md, AGENT_START.md, and llms.txt; documented data/works.json as the canonical works registry and the security.txt/warrant-canary status under docs/security/.

2026-06-10

  • SEO/discoverability pass. Fixed work-page meta descriptions that were hard-cut mid-word: build_work_pages.py now clips on a word boundary with an ellipsis via new clip_description() in code/src/site_nav.py (145 of 165 work descriptions corrected; rendered length ≤160).
  • Added Twitter Card (summary_large_image) and og:image:alt tags site-wide. Generators (build_work_pages, build_domain_pages, build_catalog, build_exports_page, build_evidence_page, build_updates_page, build_github_inventory) emit them; hand-maintained pages (index, publications, art, videos, collaborators, search, discovery, cite-verify, media, software) are covered by a new idempotent code/orchestrators/ensure_social_meta.py.
  • Added the sixth research-domain landing page domain-biomedicine.html (Genetics & Biomedicine, , 15 works) with og-biomedicine.jpg; added to sitemap_policy.py; relinked the homepage card from a raw pages/BIBLIOGRAPHY.md#… anchor to the new page.
  • Polished homepage: removed duplicate theme-color and standardized to #0c0c0e (matches manifest); tightened the meta/og description to 153 chars; added word separators between publication-card title/venue/citation spans so text extractors and screen readers no longer read them run-together.
  • New SEO invariants in code/src/seo_invariants.py (check_social_meta, check_work_descriptions) with tests in test_seo_invariants.py and test_site_nav.py; full suite 88 passing.
  • Deep-scan follow-ups: work-page fallback meta descriptions now include the title (eliminated 17 duplicate/templated descriptions across same-type works; 162/165 work descriptions now unique). Enriched ScholarlyArticle.author JSON-LD with inline @type/name/url (not just a cross-document @id) so search engines reliably attribute authorship for rich results. Applied the same word-boundary clip_description() to build_paper_pages.py (148 paper-folder pages no longer truncate mid-word). Verified site-wide: 373 JSON-LD blocks all valid, full image-alt coverage (incl. the JS-rendered art gallery via artAlt()), no broken internal links.
  • Reviewed Google Search Console (3-month window): 74 clicks / 3.25K impressions / 2.3% CTR / avg position 9; 118 indexed vs 111 not (43 "crawled-not-indexed" + 50 "discovered-not-indexed" thin/templated work pages — the description/author fixes target these). Confirmed the lone "Not found (404)" (papers/2024_PopulationSearch/) is stale (crawled before publish; now live, noindex, canonicalized). Findings + roadmap recorded in reports/seo-discoverability-audit-2026-06-10.md.
  • Added a Google image sitemap (sitemap-images.xml, new build_image_sitemap.py) declaring 942 gallery artworks for Google Images discovery — preferring the same-domain /art/*.jpg copies (939) over Flickr, since art.html renders client-side and the images are otherwise invisible to crawlers. Registered in robots.txt; well-formedness + freshness covered by test_build_image_sitemap.py.
  • Deduplicated the CEREBRUM pair: work …118 (papers/2025_CEREBRUM2, the v1.4 deposit) now sets rel=canonical + og:url to the primary entry …010 (papers/2025_CEREBRUM), consolidating ranking signals for the same paper. Added a shared WORK_CANONICAL_OVERRIDES/canonical_work_key in code/src/site_nav.py, used by both the work-page generator and the check_work_pages invariant, with a regression test.
  • Corrected three mis-attributed paper abstracts (source READMEs had the wrong paper's text), sourced from authoritative records: 2023_HoneyBeeGeneExpression (Zenodo TSGE meta-analysis abstract), 2023_AII_v1 (AII overview, recovered from the file's own schema block — the body had TrustFinder text), and 2023_ToComment (a *Physics of Life Reviews* commentary on Manrique & Walker's "To copy or not to copy?", per Semantic Scholar — not the digital-memes text it carried). All 165 work-page meta descriptions are now unique. Confirmed www→apex 301 redirect and self-canonical (no duplicate-content split). Flagged: works …010/…118 are the same CEREBRUM paper (DOI zenodo.15170907 resolves to 15231156, v1.4) — a bibliography dedup/curation decision left to the maintainer.

2026-06-04

  • Applied four strong GitHub release + Zenodo publication pairs: 2026_DeterministicTestbedSelf, 2026_RecoveringLLMPersona, 2026_Triplicate, and 2026_TemplateTextbook; bibliography **150→154**, paper folders **143→147**.
  • Refreshed represented GitHub/Zenodo publication pairs for existing works, including WhenDoBugs, MusicNeverStopped, BeeStack, BiologyTextbook, CrescentCity, and template-derived exemplars; left review-only pairings untouched.
  • Added six owned repositories to the curated software catalog (template_autoscientists, template_newspaper, template_textbook, ntqr_llm, grateful_data, cohereants); software catalog **50→56 owned**, **82→88 total**.
  • Recorded June 4 public API counts: docxology GitHub **305** public repositories, AII **51**, Zenodo exact-name **40**, Zenodo ORCID-linked **98**; treated docxology/template DOI [10.5281/zenodo.20469500](https://doi.org/10.5281/zenodo.20469500) as software/version metadata, not a bibliography work row.
  • Expanded volatile-count validation across README, AGENTS files, BIBLIOGRAPHY summaries, Discovery, llms.txt, software JSON/LD, and GitHub inventory counts.

2026-05-26

  • Thermo-nuclear documentation pass: aligned volatile counts (116 works / 109 paper folders) across llms.txt, release notes, and publications head meta; added count-consistency validation (code/src/count_consistency.py).
  • Refactored publications.html to load catalog rows from data/works.json via js/publications.js; externalized CollectionPage JSON-LD to data/publications-ld.json (166-line shell).
  • Added docs/SECURITY.md, docs/DESIGN_SYSTEM.md, reports/web_assessment_2026-05-26.md, shared nav (code/src/site_nav.py) on work and domain pages; removed Inter from body typography in favor of system-ui stack.
  • Added 2026_BiologyTextbook — *Introduction to Biology: A Generative Approach* (DOI [10.5281/zenodo.20286478](https://doi.org/10.5281/zenodo.20286478); repo docxology/biology_textbook); bibliography **116→117**; paper folders **109→110**; Computational domain **7→8**; Books **3→4**.
  • Added papers/software_table.py and papers/sync_software_html.py: full 82-row software catalog sync from pages/SOFTWARE.md to software.html + data/software-ld.json; fixed SOFTWARE.md subtotal **49→50**; biology_textbook on software surface; work-page source-repo links from metadata.json.

2026-05-19

  • Added 2026_CrescentCity — *Crescent City in Living Waves: Space, Time, People, and Minds on the Southern Cascadian Coast* (DOI [10.5281/zenodo.20286171](https://doi.org/10.5281/zenodo.20286171); repo docxology/crescent_city), filed under Cognitive Security.
  • Created the per-paper documentation set: README.md, AGENTS.md, SKILL.md, CITATION.cff, and metadata.json.
  • Registered the work in papers/paper_metadata.json, the papers/README.md index, and papers/AGENTS.md (counts + maintenance log + domain coverage).
  • Added bibliography table row 116 in pages/BIBLIOGRAPHY.md and the Cognitive Security domain index; regenerated data/works.json and bibliography exports via export_bibliography.py.
  • Resynced publications.html PUBS + JSON-LD mainEntity and regenerated downstream artifacts (search index, domain/work/catalog pages, evidence, feed, sitemap, updates).
  • Updated current counts to 116 curated works, 109 per-paper folders at the latest check.

2026-05-13

  • Added machine-readable discovery artifacts: llms.txt, CITATION.cff, codemeta.json, bibliography exports, and structured data/*.json.
  • Added domain landing pages, per-work landing pages, a generated search index, and an RSS feed.
  • Added search.html, opensearch.xml, catalog.html, data/catalog.json, GENERATED.md, and data/generated-manifest.json for human search, browser discovery, dataset discovery, and generated-file rebuild provenance.
  • Enriched generated work pages and the search index with abstracts, keywords, methods, and findings extracted from per-paper README/SKILL files.
  • Added scoped external-link reporting plus a weekly freshness workflow, Dependabot, tighter workflow permissions, and workflow concurrency controls.
  • Added updates.html, AGENT_START.md, humans.txt, .well-known/security.txt, external-link triage, live-site verification, asset-size audit, and selector-based browser smoke reporting.
  • Expanded per-work JSON-LD with citation text, DOI identifiers, keywords, documentation links, and structured publisher/about fields.
  • Added citation and evidence pages with claim confidence, caveats, maintenance ownership, and public-source reconciliation.
  • Added fresh Open Graph images for the homepage, major sections, and research domains.
  • Added source-refresh, bibliography export, software export, work-page, evidence, sitemap, reconciliation, accessibility, and visual-QA orchestrators.
  • Added GitHub Actions validation for generated files, local links, JSON-LD, sitemap targets, and the Python test suite.
  • Updated current counts to 115 curated works, 108 per-paper folders, 48 owned software repositories, 32 AII catalogued contributions, and 286 public docxology GitHub repositories at the latest API check.

2026-05-12

  • Performed repo-wide README and AGENTS audit.
  • Updated public GitHub repository count and domain figures from bibliography ground truth.
  • Verified public-source discrepancies around Google Scholar cache, AII officers, board size, and Scientific Advisory Board context.

2026-05-04

  • Renamed paper folders from author-title form to YYYY_Topic.
  • Added 2020_FacilitatorsCatechism.
  • Added shared bibliography-table parser and publication HTML synchronization script.