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

[arena-ai-coding-agent]

Summary

Replaces README.md with the estate-standard README.adoc + EXPLAINME.adoc pair, sources the BerryWiki-format wiki in docs/wikis/ (synced live to MetaManifold-WebUI.wiki.git), and provides the full paste-ready specification for GitHub Settings → Autolink references in docs/integration/autolink-references.md.

Base check

• Base is hyperpolymath/MetaManifold-WebUI:main (not the upstream
  parent; application changes go to JoshuaJewell/MetaManifold-WebUI)

Changes

• README.adoc (README.md retired):
  • Authored in AsciiDoc per standards:docs/README-EXPLAINME-STANDARD.adoc.
  • Presents the three-layer visual design progression: 1) Base R/Python design (cutadapt -> DADA2 / Swarm lanes), 2) JoshuaJewell's MetaManifold augmentation (orchestrator + DuckDB + WebUI), 3) This fork's honest estimation, exact arithmetic, scaling offsets, and epistemic status.
  • Clearly distinguishes implemented vs planned features.
  • Quick start pointing directly to EXPLAINME.adoc.
  • Third-party tools table and acknowledgements migrated into NOTICE.
• EXPLAINME.adoc (new):
  • Technical justification and claim-to-implementation map covering every README claim with exact citations, implementation notes, and caveats.
  • Dogfooding table across CLI, web UI, pipeline orchestration, and analysis layers.
  • Known gaps marked as explicit [CAUTION] blocks (statistical review outstanding, missing UI screenshots, skips in react-router/types).
  • Cross-references the wiki deep dives rather than ballooning into an unreadable file.
• docs/wikis/ (32 files, sourced per RSR convention):
  • Formatted per metadatastician/berrywiki with UUIDv7 metadata headers, hierarchy (parent), positions, and tags.
  • Three comprehensive audience sections:
    • Users: Install, First Study, Configuration Reference, Exploring Results, Analysis and Statistics, with dedicated tracks for Academics (reproducibility, citations, small-n honesty) and Lab Professionals (QC gates, database maintenance, throughput).
    • Maintainers: Operator Track (deployment, DuckDB ops, R runtime) and Steward Track (estate alignment, triage, releases).
    • Developers: Architecture Tour, Type System, Statistics Internals, Extending the Pipeline, Testing & Benchmarks, REST API.
  • Seven Deep Dives: Design Progression, Type Theory Meets Statistics, Exact Arithmetic, Maximum Likelihood & Refusals, Compositional Statistics & Offsets, Epistemic Status & Receipts, Advanced Functionality.
  • Status & Roadmap board marking all features IN PLACE / PARTIAL / COMING / BLOCKED.
  • All wiki pages carry SPDX-License-Identifier: CC-BY-SA-4.0 headers; wiki is live at https://github.com/hyperpolymath/MetaManifold-WebUI/wiki.
• docs/integration/autolink-references.md (new):
  • 22 paste-ready prefix -> URL template entries across 4 tiers (lineage/estate, upstream pipeline tools, toolchain, registries).
  • Reserved/omitted identifiers documented with rationale.
• NOTICE & CONTRIBUTING.md:
  • NOTICE updated with third-party tools table and academic acknowledgements.
  • CONTRIBUTING.md quick-start updated to reference README.adoc.
  • CHANGELOG.md updated under [Unreleased].

Engineering checklist

Required

• Conventional commit subjects (see CONTRIBUTING.md)
• New source files carry the correct SPDX header (NOTICE explains the authorship rule)
• scripts/check-spdx.sh passes (324 files covered)
• scripts/check-format.sh passes (374 files checked)
• scripts/check-blob-hygiene.sh passes (0 violations)
• No secrets, credentials, .env, or sequencing data included
• No application-logic changes hidden inside alignment/tooling PRs

As applicable

• CHANGELOG.md updated for user/developer-visible changes
• AsciiDoc delimiter balance verified (README.adoc, EXPLAINME.adoc)
• Wiki deployed and live on MetaManifold-WebUI.wiki.git

Testing

Verified locally:

• scripts/check-spdx.sh: OK (324 files covered)
• scripts/check-format.sh: OK (374 files checked)
• scripts/check-blob-hygiene.sh: OK (0 violations)
• AsciiDoc block delimiters (====, ----, ____) all balanced even counts.
• BerryWiki metadata parent graph validated: 0 dangling parents, all UUIDs unique.
• Live wiki HTTP 200 responses verified on GitHub for Home, Status and Roadmap, and Deep Dives.

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