Updates

2026-08-07

• **Two new Zenodo publications catalogued** with paper-folder documentation and regenerated bibliography, exports, work pages, feeds, sitemap, resume, accessibility, and Pages-manifest surfaces:
• **#208** PROJECT BOND — The Special-Agent Operations Compendium (, concept DOI zenodo.21843592; source repository [docxology/bond](https://github.com/docxology/bond)).
• **#209** DigiPPPiP: Digital Partner Pen Play in Parallel (, concept DOI zenodo.21815704; authors Siddhant Shrivastava, Evelyn C. Goh, Alexandra Mikhailova, and Daniel Ari Friedman).
• **Repository catalog updated**: added docxology/bond to the owned Developer Tools list; owned-repository count 94→95 and total curated software count 132→133.
• **Canonical DOI corrected** for kept ATLAS row #136 from version DOI zenodo.10362561 to concept DOI zenodo.10296601; the retired #49 duplicate remains a permanent gap.
• **Zenodo stale-version exceptions documented**: records 21418901 (SynthOBS), 20804586 (CogSecSkills), and 19139090 (retired Template/Reproducible duplicate) are not new publications and are not added.
• **Release metadata**: CITATION.cff bumped to 2026.08.07.
• **DOC-005 triage pass - ten more repositories promoted to pages/SOFTWARE.md** after manual review of the authenticated inventory (forks cleared by the owner are now reflected; inventory is 241 public repos = 154 primary + 87 forks): the six research-practice line-set repos (line_set, black_line, white_line, golden_line, red_line, witness_register, new **Research Practice** summary category, 6), the DigiPPPiP computational companion Digi-PPPiP (Other), the whole-colony simulation scaffold BeeStack (Developer Tools), the template_advanced_literature_review exemplar (Developer Tools), and crescent-city-intel (Data & Policy). Owned repositories 95->**105**; curated total 133->**143**; data/repository-classification.json uncatalogued queue 112->**101** with 4 primary-review non-fork items remaining (active_inference_power, Active_Inference_Un0, GrowthModel, multi-time - all description-less, deferred for human review).
• **DOC-004 decision R25 recorded** in data/paired-publication-decisions.json: the single new-candidate action from the paired-publication refresh (CogSecSkills v1.0.0 GitHub release paired with old concept zenodo.20804585) is **rejected** as a superseded-version false positive - bibliography row #174 already cites concept zenodo.21513316.
• **DOC-004 decisions R26-R27 recorded** in data/paired-publication-decisions.json: the 9 CogSecSkills release pairs under concept zenodo.21513316 (row #174) and 18 Codomyrmex release pairs under zenodo.21750800 (row #206) are **superseded/version-history** relations; no duplicate bibliography rows were created.
• **Authenticated GitHub inventory refresh** (241 repos, data/github-repositories.json 2026-08-07) and refreshed reports/paired_publications_2026-08-07.json; the curated flag is now computed against the full 143-row catalog.
• **Authenticated paired-publication refresh** wrote reports/paired_publications_2026-08-07.json: 402 pairs, 1 new candidate, 38 updates, and 363 items still requiring manual review under DOC-004; no candidates were auto-promoted.

2026-08-02

• **Seven new Zenodo publications catalogued** via add_zenodo_only.py as the DAF "line set" research-practice instruments plus a software release, each with full paper-folder documentation (README/AGENTS/SKILL/CITATION.cff/metadata.json + PDF) and regenerated downstream surfaces:
• **#200** The Witness Register: Co-Registration Without Aggregation (, zenodo.21754245)
• **#201** The Line Set: Holding Instruments Apart (, zenodo.21754243)
• **#202** White Line: A Typed Ledger for the Edge of the Claim (, zenodo.21754241)
• **#203** Personal Red Lines for Development (, zenodo.21754239)
• **#204** Golden Line: Toward What Matters (, zenodo.21754237)
• **#205** Black Line: Strong Work in Public (, zenodo.21754235)
• **#206** Codomyrmex: An Artificial Ecology for Agentic Software Development (, zenodo.21750800)
• **Authors populated** on all seven new rows (Friedman, Daniel Ari).
• **Zenodo uncatalogued queue cleared** (0 new remaining; the SynthOBS 21418901 and CogSecSkills 20804586 flags are stale-version duplicate detections of already-catalogued works and were intentionally not added; the AII-Ecosystem 17982447 non-canonical-DOI note remains the documented exception).
• **GitHub paired-publication sync deferred**: sync_paired_publications.py could not complete due a GitHub API rate limit (HTTP 403). codomyrmex's GitHub repo is already catalogued in SOFTWARE.md (Developer Tools); new line-set GitHub repos remain an open DOC-005 triage item pending a manual review pass.
• **Duplicate publications retired (2 rows)** after a full duplicate audit (0 duplicate DOIs; 2 genuine title/DOI duplications found and removed, keeping the canonical rows): removed **#49** (ATLAS concept-DOI zenodo.10296601, duplicate of kept **#136** /10362561) and **#193** (Template/Reproducible v1 concept zenodo.19139089, duplicate of kept **#1** /16903351). Retired numbers are left as gaps (49, 118, 193) per the repo's immutable-catalog convention — no renumbering, so every later work URL is preserved. Removed the retired paper folders (papers/2023_ATLAS/, papers/2026_TemplateApproachReproducible2/) and their work pages; paper_metadata.json 189→187; papers/README.md and BIBLIOGRAPHY header updated. Works 206→**204**, Papers 185→183. #123 (template_ approach, template_template) confirmed distinct and retained.
• **One new Zenodo publication catalogued** — **#207** THALIA: Typed Harness with Analytical Lexical-Integrated Architecture (, zenodo.21763244, 2026-08-02), a typed agentic harness for reproducible long-context memory experiments, with paired GitHub repo [docxology/thalia](https://github.com/docxology/thalia) added to pages/SOFTWARE.md (owned-repos table; software catalog rows 93→94).
• **README signposting & completeness pass**: expanded the Quick Links line and Repository Map so **every** site page is reached from the README — added research.html, reports.html, reproducibility.html, agent-verify.html, art.html, nft.html, meditations.html, about.html, exports.html and the pages/… sources (WIKIPEDIA.md, EVIDENCE.md, RESOURCES.md, VIDEOS.md, README.md); enumerated the eight domain-*.html clusters under the domains.html hub. Verified all 114 relative link targets resolve on disk (0 broken), all non-domain root .html and all pages/*.md are linked, and the Repository Map table is well-formed.
• **README + repo-organization pass**: added the 2026 line-set research-practice works and new software to the relevant domain sections, added a " Research-Practice Line Set" subsection under Computational, surfaced THALIA + Active Inference Power Suite + Codomyrmex / line-set works in the domain tables, and added Thalia + the line-set repos to the highlighted-repositories list. Verified AGENTS.md-referenced orchestrators (regenerate_docs, sync_publications_html, sync_software_html, export_bibliography, export_agent_data, sync_scholar_metrics) all exist.
• **Accessibility/usability fix — site header was unusable**: the global
• Bibliography **199→206**; paper folders **181→188**.
• CITATION.cff version/date-released bumped to 2026.08.02.

2026-07-30

• **One new Zenodo publication catalogued** via add_zenodo_only.py: **#199** Active Inference Power Suite: Conditional Statistical Power under Controlled Generative Settings (, zenodo.21695160), with full paper folder documentation and regenerated downstream surfaces.
• **Two existing works updated** to newer Zenodo records (same work, re-deposited): **#174** CogSecSkills (20804585 → 21513316, domain corrected to ) and **#198** SynthOBS & FractiSynth (21418687 → 21418782). Duplicate rows #200–#201 retired.
• **Comprehensive repo audit**: Zenodo uncatalogued queue cleared (0 remaining), paired-publication scan (0 new pairs), all local validate_repo.py checks pass (39/40 — live-site mismatch at 197 vs 199 is expected pre-push), 216 pytest green, 1540/1540 static accessibility passes, 0 asset-size warnings, all count-consistency surfaces aligned.
• Bibliography **197→199**; paper folders **180→181**.

2026-07-24

• **Repo-wide functional and signposting audit implemented**: Pages growth reports are date-stable control metadata across UTC rollovers; release-integrity now records explicit deployment-pending reasons and supports a strict --require-deployed gate; accessibility commands use the supported --check flag; public-page SEO guidance distinguishes indexable pages from intentional paper/redirect exceptions; cache-buster documentation matches the generated layer; and the historical maintenance table moved out of always-loaded AGENTS.md.
• **Regeneration tail made one-pass idempotent**: build_generated_manifest.py now runs before build_agent_index.py, so the agent route manifest hashes the current command matrix on its first pass; a final manifest pass still closes the release-integrity envelope. The ordering is regression-tested in test_regenerate_all.py.

2026-07-17

• **Compact video projection and repository triage added**: the interactive timeline now loads generated data/videos-index.json (VideoIndex.v1, 1127 compact records) while the complete data/videos.json remains available for downloads and detail pages; the repository classification queue now preserves description, language, topics, privacy, update, and derived description-quality fields for all 292 uncatalogued repositories (45 missing, 43 short, 204 substantive descriptions) without auto-promotion.
• **Operating runbooks expanded**: added repository-classification, CV release, evidence-refresh, accessibility/browser/visual QA, and live-verification runbooks; linked them from docs/README.md and AGENT_START.md. The ordered regeneration chain now re-runs asset and static accessibility reports after catalog rendering so generated report checks remain current when the catalog grows.
• **Regeneration pipeline made genuinely idempotent**: fixed local-vs-UTC report selection at the date boundary, moved the agent manifest behind its report and Pages dependencies, and added body-aware timestamp reuse across generated snapshots, exports, CV, feeds, and indexes. A complete second regenerate_all.py pass now produces zero file-content changes; the Pages artifact also treats GENERATED.md as control metadata so the integrity tail cannot invalidate its own manifest.
• **Progressive browser QA added**: browser_qa.py now exercises no-JavaScript fallbacks, mobile menu Escape/focus, publication filtering and sorting, gallery lightbox focus, reduced motion at 320px, forced colors, console/page errors, and YouTube iframe origin/title/referrer policy. The fresh report passes 7/7; browser smoke passes 10/10 and visual QA covers 26 screenshots.
• **Artwork gallery payload split**: added generated data/artworks-index.json (942 grid records, 712 KiB versus the 3.1 MiB full export) and lazy full-detail loading for description search and lightbox resolution links. The complete data/artworks.json export remains available for agents and downloads.
• **Backlog and documentation cleaned**: removed the completed stale issue-sync item from TODO.md, kept remaining release work as recurring gates, corrected the animation documentation's obsolete inline-script reference, and documented the GitHub Pages meta-CSP frame-ancestors limitation.
• **Public-source refresh completed without unreviewed promotion**: refreshed the dated public-source/inventory, repository, coverage, and pairing reports; the current pairing scan found one represented update and no new or ambiguous rows. Repository validation passes 1531/1531 static accessibility checks, 186 tests, the 17/17 live snapshot gate, strict report validation, Pages artifact checks, and GSC preflight.

2026-07-16

• **Service worker v20 — content data is network-first**: data/*.json and search-index.json were served cache-first, and each page fetches them at a stable ?v= query that does not change when the data does — so a returning visitor kept seeing the *previous* publication list (e.g. 193 works after #195 was added) until the SW version happened to bump. These content-data requests are now network-first (cache fallback for offline), matching navigations; static assets (JS/CSS/images/fonts) stay cache-first for speed. Bumped v19 → v20 to clear existing stale caches. This is why a freshly-added publication now appears immediately.
• **New publication catalogued — Active FractalRabbit**: added *"Active FractalRabbit: A Synthetic Benchmark for Belief Filtering Under Sparse Waypoint Observations"* (Daniel Ari Friedman, Zenodo 2026-07-13, canonical concept DOI 10.5281/zenodo.21330636) as work #195 via add_zenodo_only.py. Created papers/2026_ActiveFractalRabbit/ (README/AGENTS/SKILL/CITATION.cff/metadata.json + PDF), the works/…195.html page, and regenerated the bibliography, works/software exports, catalog, search index, feed, sitemaps, and counts (bibliography works 193 → 194). check_zenodo_uncatalogued.py now reports the bibliography caught up (0 uncatalogued). Scope note: "0 uncatalogued" covers the Zenodo/ORCID deposit channel (DAF's primary archival target) — curated software (SOFTWARE.md) and presentations are deliberately-curated subsets, not auto-swept, and Google Scholar citation metrics (data/scholar-snapshot.json, as_of 2026-06-09) require DAF's own signed-in browser fetch per repo policy and were not updated. The record-17982447 non-canonical-DOI note is the documented AII-Ecosystem yearly-snapshot exception and is intentionally unchanged.
• **add_zenodo_only.py DOI fix**: the tool wrote the version-specific DOI into the per-paper folder files (README/AGENTS/SKILL/CITATION.cff/metadata.json) while the bibliography and paper_metadata.json used the canonical concept DOI — splitting one work across two DOIs and failing test_paper_readme_contracts.py. Added a canonical_doi(rec, meta) helper (concept-DOI-first, mirroring the bibliography derivation) and routed every folder renderer through it; the version id is retained separately as record_id. Future Zenodo-only additions are now concept-DOI-consistent by construction.
• **CSP inline-script breakage fixed (art gallery restored)**: the script-src 'self' CSP deployed 2026-07-12 silently blocked the inline <script> blocks still shipping on art.html, videos.html, search.html, repositories.html, repositories-forks.html, and index.html — /art rendered zero of its 942 artworks and its search box only surfaced site-wide paper suggestions. All six pages' scripts externalized to js/art-gallery.js, js/videos-page.js, js/search-page.js, js/repo-inventory.js (shared by both repo pages), and js/index-page.js.
• **Art gallery search is art-local again**: new data-local-search attribute on the /art search input opts it out of the site-wide search-index.json autocomplete in js/interactive.js; gallery filtering (title/description/tags over all 942 works) is handled by js/art-gallery.js. Also fixed a latent error-path bug (getElementById('empty') → emptyState) and a duplicated tts-controls.js include.
• **Lightbox double-advance fixed**: the /art lightbox sort/size/nav controls carry data-* attributes already delegated by js/interactive.js to window.* globals; js/art-gallery.js was additionally addEventListener-wiring the same buttons, so each ‹/› click advanced two artworks. art-gallery.js now wires only the search input, Escape/arrow keys, and overlay-click and defers the delegated controls to interactive.js (caught by cross-vendor review).
• **videos.html skip-link**: inline onfocus/onblur (CSP-blocked) replaced with a CSS :focus reveal rule.
• **Font loading un-broken CSP-safely**: the media="print" onload="this.media='all'" pattern (blocked by CSP, so Google Fonts never applied on nine pages) replaced with media="print" data-media-swap="all" + an external swap in js/interactive.js; optimize_font_loading.py updated to emit and migrate to the new pattern.
• **publications.html search input**: CSP-blocked inline oninput="filterPubs()" replaced with addEventListener wiring in js/publications.js.
• **Service worker v19**: cache bumped; new per-page JS modules added to the precache list.

2026-07-12 (session 5)

• **Non-render-blocking Google Fonts**: All 17 HTML pages with Google Fonts links converted to media="print" onload="this.media='all'" pattern, eliminating render-blocking CSS on first paint. New code/orchestrators/optimize_font_loading.py orchestrator.
• **Twitter Card tags on about.html**: Added twitter:card, twitter:title, twitter:description, twitter:image meta tags for social sharing parity with OG tags.
• **apple-touch-icon optimized**: Reduced from 77KB to 39KB (48% reduction) via PNG quantization to 128 colors, with no visible quality loss at 180x180.
• **extract_paper_texts.py error logging**: Silent except Exception: continue now logs the exception with page number, image index, and PDF filename to stderr before continuing, preventing silent extraction failures.
• **Descriptive image alt text**: Paper page thumbnail alt text now uses "Figure from [paper_name], page N" instead of raw filenames, improving screen reader usability and SEO.
• **Service worker v18**: Cache version bumped to serve updated JS assets (CSP-compliant scripts, search badges, count badges).

2026-07-12 (session 4)

• **CITATION.cff generated for all 176 papers**: New generate_citation_cff.py script creates CFF 1.2.0 files from metadata.json. 47 papers that were missing CITATION.cff now have it. Year extracted from folder names for older papers. Multi-line author format with ORCID for DAF.
• **2024_BioFirm PPTX extraction**: Downloaded BIOFIBIOFIRM_v2.pptx from Zenodo, extracted 11 slides of text + 8 images using python-pptx. 173 of 176 papers now have full_text.md (98.3% coverage).
• **Content-Security-Policy deployed**: CSP meta tag (script-src 'self') now on all 23 indexable HTML pages, blocking inline event handlers and inline <script> blocks. Documented in docs/security/security-posture.md.
• **Inline event handlers eliminated**: all 68 onclick/onchange/onsubmit handlers across 23 pages migrated to data-* attributes wired via addEventListener in js/interactive.js. New code/orchestrators/migrate_inline_handlers.py orchestrator.
• **rel="me" social verification links** expanded from 3 pages to all 21 indexable pages (Scholar, ORCID, GitHub, LinkedIn, YouTube, Wikidata, Bluesky).
• **hreflang alternate links** expanded from 1 page (index.html) to all 21 indexable pages.
• **External js/menu-esc.js**: menu Escape-to-close handler moved from inline <script> to external file for CSP compliance.
• **Service worker bumped to v17**: cache version updated for new JS assets.
• **Accessibility audit enhanced**: accessibility_audit.py now checks for no_inline_handlers as a gate (16 checks, up from 15). All 23 pages pass.
• **art.html nav-toggle button**: added missing .menu-btn for keyboard-accessible menu toggle on the art gallery page.
• **New orchestrators**: deploy_seo_security.py (idempotent CSP/rel-me/hreflang deployment), migrate_inline_handlers.py (inline handler → data-attribute conversion).
• **Shared head extras**: HEAD_EXTRAS constant in code/src/site_nav.py centralizes CSP + rel-me + hreflang + dns-prefetch for generated HTML templates (domain, work, paper, video pages).
• All generated surfaces, sitemap, manifest, and asset-size report refreshed. All validation + 154 tests green.

2026-07-12 (session 3)

• **Image thumbnail previews on paper landing pages**: image_gallery_link() in build_paper_pages.py now shows up to 6 thumbnail previews of extracted figures with lazy loading and a "+N more" indicator. All 176 paper pages regenerated.
• **CSS classes for thumbnails**: .image-thumbs, .thumb-link, and .muted added to style.css, replacing inline styles for cleaner maintenance and consistent rendering.
• **Search index image_count**: build_search_index.py now includes image_count for works with extracted images (140 works). Search results page shows "Full Text" and "N Images" badges on matching works.
• **llms.txt stale counts corrected**: 171→172 full text papers, 139→168 image galleries, 8986→9938 images.
• **PPTX text extraction**: Extracted text from BIOFIBIOFIRM_v2.pptx (11 slides) for 2025_BiofirmDevelopmentWith. 172 of 176 papers now have full_text.md (97.7% coverage).
• All generated surfaces, sitemap, manifest, and asset-size report refreshed. All validation + 154 tests green.

2026-07-12

• Added work **#194 "Prior Cognitive Art"** (zenodo.21316510, docxology/prior_cognitive_art v0.1.0) via the canonical sync_paired_publications.py --apply path. Paper folder, bibliography row, work page, domain page, search index, sitemap, and all generated surfaces updated.
• **Enhanced full-text extraction pipeline**: extract_paper_texts.py now embeds inline image references in full_text.md at the correct page positions, so readers and crawlers can discover extracted figures in context.
• **171 papers** now have full_text.md (was 166 — gained 5 from ODT/DOCX/PDF source extractions)
• **8,986 images** extracted across **139 papers** (was 3,057 across 136)
• **8,924 image references** embedded inline in full_text.md with 0 broken links
• Downloaded and extracted text from 4 Zenodo ODT/DOCX transcript files and 1 misnamed PDF
• format_markdown() now accepts an images parameter and groups image refs by page
• extract_images() now returns (page_num, filename) tuples for page-aware embedding
• **Image sitemap expansion**: build_image_sitemap.py now includes paper-extracted figures in sitemap-images.xml (9,928 total images, was 942 — 139 paper pages with image galleries)
• **Full-text extraction pipeline**: new code/orchestrators/extract_paper_texts.py extracts page-level text and embedded images from all paper PDFs using PyMuPDF (with OCR fallback via tesseract for scanned PDFs).
• **166 papers** now have full_text.md with complete page-by-page text extraction
• **3,057 images** extracted to per-paper images/ subdirectories across **136 papers**
• **0 errors** across all 166 extractions (10 papers have no PDF — Zenodo-only metadata, slides, or non-PDF artifacts)
• Paper landing pages (papers/*/index.html) now link to full_text.md and the images/ gallery
• Work pages now include JSON-LD encoding field (Schema.org TextObject) for all 166 works with full text
• Search index includes full_text_url for all 166 works with extracted text
• papers/README.md updated to document full_text.md and images/ as standard folder contents
• llms.txt updated with full-text extraction pipeline link
• Fixed regenerate_all.py to use sys.executable instead of hardcoded python3 (was breaking on Python 3.9 vs 3.14 datetime.UTC import)
• Fixed build_current_counts.py Python 3.9 compatibility (datetime.UTC → datetime.timezone.utc)
• Fixed build_resume.py to gracefully skip PDF generation when reportlab is not installed
• Fixed validate_repo.py to skip full_text.md files in local-link validation (academic paper internal references)
• Fixed build_sitemap.py to not list /papers/ URLs (SEO invariant compliance)
• All 22 local generated surfaces regenerated (bibliography, publications, software, domains, works, paper pages, exports, evidence, catalog, search index, RSS feed, sitemap, manifest)

2026-07-05

• Comprehensive interactive-layer buildout across all 23 indexable pages:
• **Text-to-Speech (TTS)**: Web Speech API integration (js/tts-controls.js) — floating control panel, speed/voice selection, paragraph highlighting, keyboard shortcut T
• **Interactive features** (js/interactive.js): reading progress bar, scroll-to-top button, keyboard shortcuts overlay (?), section anchor copy-links, search autocomplete from search-index.json, image lazy loading, external link safety
• **+515 lines CSS** for all new components with responsive, print, and reduced-motion overrides
• **Service Worker v16** — caches new JS modules, drops stale cache
• **Performance**: 5 hero-art image preloads, resource hints (dns-prefetch, prefetch) across all pages, preconnect for Scholar/ORCID
• **SEO**: rel="me" social profile verification links, hreflang support, WebPage JSON-LD on homepage
• **Docs**: SKILL.md, docs/design/components/tts.md, docs/design/animations.md; updated AGENTS.md with WEB DEVELOPER role, CLAUDE.md with interactive layer commands, design-system docs with new components
• 5 noindex redirect stubs intentionally skipped (about, research, meditations, nft, google verification)

2026-07-01

• Massive metadata enrichment sweep: all 164 paper folders now have extended schema (domain, type, methods, key_findings, related_papers, checked_at) via batch_enrich_metadata.py. 44 previously-missing metadata.json files created, 119 existing ones extended with paper-specific content.
• Multi-agent triple audit completed: metadata completeness (164/164 pass), navigability (all SKILL.md cross-references valid, all bibliography rows linked), domain accuracy (0 discrepancies), HTML output quality (26 root pages + 183 work pages well-formed, JSON-LD valid), live site parity (14/14 checks pass, no drift).
• Quality improvement pass: replaced 3 placeholder key_findings, fixed 55 truncated findings with sentence-boundary extraction, replaced generic domain-template methods with paper-specific methods for 163 papers (e.g. "Uniparental marker haplotype analysis", "Lean 4 theorem proving", "CPRA legal analysis").
• Added code/orchestrators/batch_enrich_metadata.py (bulk metadata generation), code/orchestrators/improve_metadata_quality.py (paper-specific methods/findings), code/src/paper_metadata_schema.py (dataclass schema).
• Full validate_repo.py --strict-reports pipeline passes (30+ checks including browser smoke, accessibility, visual QA, live-site verification, sitemap, search index, external links).
• Added works **#180 "Sortition Upstream of NTQR"** (zenodo.21083779), **#181 "Exploratory Data Analysis: A Reproducible Notebook Template"** (zenodo.21086292), **#182 "A Domain Language for Specifying Controlled Methods"** (zenodo.21086548) — all Computational, with paper folders and full metadata.

2026-06-29

• Added work **#179 "Mapping William Blake's Works"** (zenodo.21047573, docxology/blake v0.1.0) via the canonical sync_paired_publications.py --apply path, plus benign checked_at metadata bumps on existing rows. Full local regenerate (works.json, exports, publications, work/domain/paper pages, resume, claims, catalog, search index, feed, sitemap, counts) and live-site snapshot refresh; validate_repo + pytest green. Also fixed 32 malformed bare-domain markdown links in reports/publishing_status_megaindex.md.

2026-06-27

• Added work **#178 "AlphaCOGANT: Recursive Corporate Self-Improvement as Active Inference"** (zenodo.20976824, docxology/alphacogant v1.0.1) with paper folder, PDF, and work page; updated "A template/ approach to Reproducible Generative Research" to Zenodo version v1.0.9. Regenerated the dependent layer and refreshed the live-site verification snapshot.
• build_work_pages.py now renders a **Platform availability card** on every canonical work page (Zenodo/GitHub/arXiv/OSF/HuggingFace/Software-Heritage/PyPI/site), driven by a new data/publishing-status.json; added reports/publishing_status_megaindex.md, a publishing-status mega-index across 272 items (works + software) with per-platform coverage and gaps. Began archiving origins to Software Heritage via anonymous Save Code Now.

2026-06-26

• Added works **#176 "A Living Meta-Analysis of the Modafinil Literature"** and **#177 "Refinement of Gold"** via the paired GitHub+Zenodo scan, with new paper folders (README/AGENTS/SKILL/CITATION.cff/metadata.json) and Zenodo PDFs; refreshed checked_at metadata on 27 existing paired works. Regenerated bibliography exports, publications/works/paper/domain pages, catalog, search index, feed, sitemap, resume, claims, evidence/reconciliation, and current counts; live-site snapshot refreshed.

2026-06-24

• Added work **#175 "Realizing Emptiness: Operational Surrogates for No-Self-Evidence, QRF Opacification, and Bayesian Model Reduction"** (zenodo.20834846, docxology/realizing_emptiness v1.0.0) via sync_paired_publications.py --apply; refreshed checked_at metadata and software links for 25 existing works; fixed the pages/BIBLIOGRAPHY.md paper-folder prose count (156→157).
• Added code/orchestrators/regenerate_all.py: a single-command, dependency-ordered, local-only write-mode counterpart to validate_repo.py's --check sequence (manifest last), replacing manual whack-a-mole after a publication-sync apply. refresh_bibliography_counts now also keeps the "**N** indexed paper folders" prose current. validate_repo.py now runs sync_scholar_metrics.py --check, catching Scholar-metric drift across README/BIBLIOGRAPHY/PROFILE/LINKS/DISCOVERY (previously unguarded).
• Pruned superseded dated QA screenshot sets under reports/visual-qa and reports/browser-smoke (validation only reads the latest); reports/ 100 MB → 40 MB. add_zenodo_only.py now runs regenerate_all.py automatically after adding records.
• Softened unguarded external/domain prose counts that would drift as external repos grow (codomyrmex module counts, COGSEC bio paper/book counts); fixed regenerate_all.py's report-producer ordering so write-mode indexes don't go stale relative to the dated reports they link.

2026-06-22

• Synced the **CogSecSkills** publication (zenodo.20804585, ) and hardened publication intake.

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.
• Design/a11y pass: reconciled design-system.md to the actual style.css (corrected background/radius/body-font/focus-color tokens, documented previously-missing tokens); added mobile-menu aria-expanded toggling, ESC-to-close, and a 44px WCAG touch target across all 20 nav pages and their generators; fixed heading-hierarchy skips (h1→h3/h2→h4) on domain and index pages; added aria-labels to 3 unlabelled search inputs; tokenized 26 hardcoded gold rgba() values into 14 --gold-NN tokens (no visual change); accessibility_audit.py now enforces single-h1, no-heading-skips, and form-control-labels (22/22 pages pass).
• Migrated the site body font from Georgia serif to **Inter** to match the design system (Playfair Display headings unchanged); centralized the duplicated menu-ESC handler into site_nav.MENU_ESC_SCRIPT; removed 26 lines of verified-dead CSS (duplicate footer block, zero-reference selectors) after confirming the two-layer base+newspaper override structure is intentional, not duplication.

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.