docs: make the GitHub wiki a lightweight index of the docs site

[bioedca]

Why

The repository has a wiki that is currently empty, so it competes with the MkDocs site as a documentation destination and gives anyone who lands there nothing. Rather than disabling it, it should become a thin signpost that routes readers to the real documentation.

Evidence

• The wiki is enabled and empty; the canonical documentation lives at https://bioedca.github.io/tether/, published with mike and versioned.
• Search engines and GitHub's own UI surface a repo wiki independently of the Pages site, so an empty wiki is a live dead end.
• The docs site is healthy again as of 2026-07-30 (ci(docs): add a liveness guard so a Pages source change cannot silently unpublish the docs site #325): /latest/, /versions.json and every page URL below return 200, and the served generator is mkdocs-1.6.1, mkdocs-material-9.7.7. The version selector exists again, so the version-selector deliverable is satisfiable.
• The index may only link pages that exist. docs/install.md, docs/tutorial.md and docs/citing.md are not on main — they are the deliverables of open docs: add the end-user installation guide #167, docs: add the guided first run (tutorial) and its sample dataset #176 and docs: make CITATION.cff produce a real citation, and add a per-method citing page #162 respectively, and /latest/install/, /latest/tutorial/ and /latest/citing/ all return 404 today. An index naming them cannot pass its own "every link resolves" criterion.

Deliverables

• Wiki Home page — one screen: what Tether is in two sentences, a prominent link to https://bioedca.github.io/tether/, and a short link list to the main sections that exist and are in the nav today: Does Tether fit my data? (compatibility), Roadmap, Command line (CLI), Exports, Analysis parameters, Project store, Validation & benchmarks, Glossary, Troubleshooting, Packaging, Releasing, Architecture decisions, Stability policy, Privacy policy.
• Re-derive that list from mkdocs.yml nav: at implementation time rather than copying it from here — docs: add the end-user installation guide #167 (Install), docs: add the guided first run (tutorial) and its sample dataset #176 (Tutorial) and docs: make CITATION.cff produce a real citation, and add a per-method citing page #162 (Citing) each add a page, and each should be added to the index when its page lands, not in advance. Do not add a link this issue cannot load.
• A one-line statement at the top that the wiki is an index only and the docs site is canonical, so nobody adds content here.
• Link the docs site's version selector explicitly, so readers know how to match their installed release.

Acceptance criteria

• The wiki Home page renders with every link resolving (check each by loading it).
• The page contains no substantive documentation content — only orientation and links. Anything longer than a paragraph belongs on the docs site.
• No link points at a dev docs tree; all point at latest or the un-versioned root that redirects to it.

Constraints

• This is an index, not a second home. Any content added here will drift out of sync with the docs site, which is exactly the failure mode that made the wiki worth addressing.
• Wiki content lives in a separate git repository (.wiki.git) and is not covered by this repo's REUSE configuration or CI — it will not be linted or link-checked, which is another reason to keep it to a single short page.
• latest currently aliases dev. versions.json holds exactly [{"version":"dev","title":"dev","aliases":["latest"]}] because v1.0.0 has not been cut and docs.yml refuses to alias latest to a pre-release. Linking /latest/... therefore satisfies the "no dev tree" criterion above and is the correct thing to write — do not "fix" it to a version number, and do not link /dev/... directly.
• Prior work exists; do not restart from zero and do not resume it wholesale. Closed-unmerged draft PR docs(docs): add reviewed GitHub wiki index #251 left branch docs/issue-189-github-wiki-index at 350cc37 on origin, carrying reusable files (.github/workflows/wiki.yml, wiki/Home.md, the mkdocs.yml and docs/adr/README.md edits). It is +985/−0 across 8 files, roughly 6.5× the size:S budget — see the 2026-07-29 comment for the per-file disposition. Harvest from it, then let the branch be deleted. refs/adr-reservations/0058 (44bb596) is still held on origin; decide its disposition in the same PR — under the current contract an ADR is authored only when the issue carries needs:adr, and this issue does not.

Meta

• Priority: P2
• Effort: S
• Autonomy: agent-can-do-alone
• Milestone: M10 — Docs & community
• Area: docs
• Depends on: none
• Related: chore: repository metadata and project-state hygiene for a public 1.0 #184 (repo hygiene — the wiki was originally proposed for disabling; this supersedes that), ci(docs): add a liveness guard so a Pages source change cannot silently unpublish the docs site #325 (the docs site the index points at; restored 2026-07-30), docs: add the end-user installation guide #167 / docs: add the guided first run (tutorial) and its sample dataset #176 / docs: make CITATION.cff produce a real citation, and add a per-method citing page #162 (each adds a page this index should link after it lands)

Grooming status — 2026-07-27

• Status: ready.
• Delivery path (decided 2026-07-27): checked-in wiki source in this repository plus a reviewed
  publishing workflow that mirrors it to the separate .wiki.git repository. This discharges the
  2026-07-22 blocker, which required one PR-governed delivery path to be explicit before this issue
  could enter the autonomous swarm.
• Scope guard: the wiki stays a thin index pointing at the MkDocs site; it must not duplicate
  content that would then drift (chore: repository metadata and project-state hygiene for a public 1.0 #184's 2026-07-20 override). The wiki also stays enabled — that
  same override supersedes the earlier has_wiki=false proposal, and this issue and chore: repository metadata and project-state hygiene for a public 1.0 #184 must not be
  executed in a way that cancels each other.
• Implementation note: the .wiki.git repository is currently uninitialized, so the first publish
  creates it. Confirm the publishing token/permission model before writing the workflow; do not weaken
  repository permissions to make the push succeed.
• Autonomy: agent-can-do-alone.
• Dependencies: none. docs: add the end-user installation guide #167, docs: add the guided first run (tutorial) and its sample dataset #176 and docs: make CITATION.cff produce a real citation, and add a per-method citing page #162 are not blockers under the 2026-08-02 narrowing — the
  index links only pages that exist, and each of those issues adds its own link when it lands.
• Ready condition: met on the delivery-path axis; needs a fresh exact-scope tether-agent-ready
  marker, because the 2026-08-02 narrowing edits this body and voids the 1f6176d7… approval.

[bioedca]

Maintainer decision (2026-07-27)

Wiki delivery path: checked-in wiki source in this repository plus a reviewed publishing workflow. This resolves the blocker recorded in the 2026-07-22 grooming note ("do not place this issue in the autonomous swarm until one PR-governed delivery path is explicit").

The chosen path, for the record:

• The wiki's content lives in this repository as ordinary tracked Markdown, so it is reviewed through a normal Tether branch/PR, covered by REUSE, and reachable by the docs link checker (ci(docs): add the internal link checker, a rendered-site artifact and a static docs-example check #183) and the prose linter (ci(docs): add the prose/spell linter and absorb the churn across the existing corpus #185) when those land.
• A workflow publishes that source to the separate .wiki.git repository. Publishing is a mechanical mirror step, never a place where content is authored.
• The wiki stays a thin index: a landing page pointing at https://bioedca.github.io/tether/ and its main sections. It must not duplicate content that would then drift — that constraint from chore: repository metadata and project-state hygiene for a public 1.0 #184's override is unchanged.

Rejected alternatives, so they are not revisited:

• Maintainer-only manual initialization — keeps docs: make the GitHub wiki a lightweight index of the docs site #189 permanently outside the swarm, and the page would never be linted or link-checked.
• Disabling the wiki — reverses chore: repository metadata and project-state hygiene for a public 1.0 #184's explicit 2026-07-20 override, which decided the wiki stays and becomes an index of the docs site.

Implementation note for whoever picks this up: the .wiki.git repository is currently uninitialized, so the first publish has to create it. Confirm the publishing token/permission model before writing the workflow, and do not weaken repository permissions to make the push succeed.

This issue is now unblocked and agent-executable; its body's grooming block has been updated to match, and a fresh exact-body approval follows.

[bioedca]

Maintainer approval — approved for autonomous execution.

Delivery path decided 2026-07-27 (checked-in wiki source + reviewed publishing workflow); the 2026-07-22 swarm blocker is discharged.

The acceptance criteria, scope and non-goals in the body above are approved as written. This approval binds that exact title/body snapshot; any edit to either invalidates it and requires a fresh approval comment.

Approved scope digest: 1f6176d7982f

[bioedca]

🧰 @bioedca's The Test Pilot is packing a handoff

State is preserved. A new worker needs a recorded transfer before touching it.

• Automated Codex worker: codex-test-pilot-87449b82
• Work item: bioedca/tether#189
• Lease state: handoff
• Lease ends: 2026-07-28T03:15:40Z
• Branch: docs/issue-189-github-wiki-index
• Approved scope: 1f6176d7982f
• Approval comment ID: 5087571526

This persona is automated coordination state, not maintainer approval.
If this lease expires, the dispatcher will inspect the work before requeueing it.