docs: replace README with estate README.adoc + EXPLAINME.adoc pair, source wiki, and elaborate autolinks

.gitignore

@@ -266,6 +266,8 @@ docs/*
 !docs/owner-review-2026-09-25.md
 !docs/integration/
 !docs/integration/**
+!docs/wikis/
+!docs/wikis/**
 !docs/formal/
 !docs/formal/**
 !docs/triage/

CHANGELOG.md

@@ -12,6 +12,34 @@ types, tests, infrastructure, and alignment.
 
 ## [Unreleased]
 
+### Added — the README/EXPLAINME pair, the wiki, and the autolink specification (2026-09-26)
+
+- **`README.adoc` replaces `README.md`**, per the estate README/EXPLAINME authoring
+  standard (`standards:docs/README-EXPLAINME-STANDARD.adoc`). The README is now the
+  three-layer design history — base R/Python design around raw DADA2, the origin
+  MetaManifold augmentation (JoshuaJewell), and the fork's honesty/typing steps — with
+  diagrammatic progression and shipped/planned markers throughout. The configuration
+  chapters moved to the wiki (they made the README unreadable); the third-party tools
+  table and acknowledgements moved into `NOTICE` (their natural home).
+- **`EXPLAINME.adoc`** (new): the receipts file — claim→implementation→caveat map over
+  every README claim, the dogfooding table, known gaps as CAUTION blocks, and an
+  evidence index. The type-theory/enhanced-statistics deep material deliberately lives
+  in the wiki; EXPLAINME cross-references it rather than re-deriving it.
+- **The GitHub wiki is now the full BerryWiki-format documentation**
+  (`metadatastician/berrywiki` page format: hidden metadata blocks, generated
+  `_Sidebar.md`), sourced from `docs/wikis/` and synced to `MetaManifold-WebUI.wiki.git`:
+  three audience sections (users — with academics and lab-professional tracks; platform
+  maintainers — operator and steward tracks; developers), seven deep dives (design
+  progression, type theory meets statistics, exact arithmetic, maximum likelihood and
+  refusals, compositional statistics and offsets, epistemic status, advanced
+  functionality), and a Status-and-Roadmap board marking everything IN PLACE / PARTIAL /
+  COMING / BLOCKED.
+- **`docs/integration/autolink-references.md`** (new): the complete elaboration of the
+  repository's Settings → Autolink references set (lineage/estate, upstream tools,
+  toolchain, registries), paste-ready and machine-readable, with reserved/omitted cases
+  reasoned. Application in Settings needs Administration permission (one human pass);
+  the file is the source of truth for it.
+
 ### Added — the three deferred ILR bases are implemented, with proofs (#20, 2026-09-26)
 
 - **`phylogenetic` (PhILR), `sequential_binary_partition` and `balance_dendrogram`** are

CONTRIBUTING.md

@@ -41,7 +41,7 @@ bun test                    # unit + integration batteries (no DOM lane)
 bun run bench/              # benchmark harness (informational)
 bun run check               # all three in sequence — must be green
 
-# Full application (requires Julia + R/renv per README.md § Prerequisites)
+# Full application (requires Julia + R/renv per README.adoc § Quick start)
 ./install.sh                # upstream flow
 ./start.sh
 ```

NOTICE

@@ -29,11 +29,47 @@ unambiguous; it is not a claim of copyright ownership either way.
 ## Third-party components
 
 MetaManifold orchestrates, but does not vendor, third-party command-line
-tools (cutadapt, DADA2, SWARM, vsearch, cd-hit-est, R/vegan). Each tool
-retains its own licence; see `README.md § Third-party tools` for the
-runtime dependency list and upstream references. Frontend npm dependencies
-are declared in `frontend/package.json` / `frontend/bun.lock` under their
-own licences.
+tools. Each is fetched from its upstream source by `install.sh` and is
+subject to its own licence; no third-party binaries are included in this
+repository.
+
+| Tool | License | Source |
+|---|---|---|
+| [cutadapt](https://github.com/marcelm/cutadapt) | MIT | PyPI |
+| [FastQC](https://github.com/s-andrews/FastQC) | GPL v3 | Babraham Bioinformatics |
+| [MultiQC](https://github.com/MultiQC/MultiQC) | GPL v3 | PyPI |
+| [DADA2](https://benjjneb.github.io/dada2/) | LGPL v3 | Bioconductor |
+| [swarm](https://github.com/frederic-mahe/swarm) | GPL v3 | GitHub Releases |
+| [vsearch](https://github.com/torognes/vsearch) | GPL v3 | GitHub Releases |
+| [cd-hit](https://github.com/weizhongli/cdhit) | GPL v2+ | GitHub Releases / apt |
+
+R/vegan and the R runtime are system components under their own licences
+(GPL family). Frontend npm dependencies are declared in
+`frontend/package.json` / `frontend/bun.lock` under their own licences.
+
+## Acknowledgements and lineage
+
+This pipeline draws on the following prior work:
+
+- **Frédéric Mahé**: [Fred's metabarcoding pipeline](https://github.com/frederic-mahe/swarm/wiki/Fred's-metabarcoding-pipeline)
+  informed the overall workflow architecture, namely the sequencing of
+  primer trimming, `swarm.jl`, vsearch-based taxonomy assignment, and the
+  final table merge/filter stages.
+- **Benjamin J. Callahan _et al._**: [DADA2 tutorial](https://benjjneb.github.io/dada2/tutorial.html),
+  used under [CC BY 4.0](https://creativecommons.org/licenses/by/4.0/), on
+  which `dada2.jl` and its modules are based.
+
+The following colleagues at the **Department of Parasitology, Charles
+University** (Faculty of Science, BIOCEV, Vestec, Czech Republic)
+contributed to this work:
+
+- **Mgr. Jiří Novák** (supervisor): scripts from which several modules and
+  configurations were adapted.
+- **doc. Mgr. Vladimír Hampl**: provided laboratory access and resources.
+- **Mgr. Paulína Pristašová**: <3.
+
+Copyright © 2026 Joshua Benjamin Jewell (origin design) and the
+hyperpolymath fork authors.
 
 ## Notices required by AGPL-3.0