hyperpolymath · hyperpolymath · Sep 26, 2026 · Sep 26, 2026 · Sep 26, 2026 · Sep 26, 2026
@@ -268,6 +268,11 @@ docs/*
 !docs/integration/**
 !docs/formal/
 !docs/formal/**
+!docs/triage/
+!docs/triage/**
+# …but the generated PR-#7 stack patches are derived artefacts: regenerate
+# with docs/triage/pr7-split/make-stacks.sh instead of committing them.
+docs/triage/pr7-split/patches/*.patch
 
 # Test + benchmark run artifacts (not the committed fixtures/baselines)
 frontend/tests/results/

@@ -0,0 +1,222 @@
+<!--
+SPDX-License-Identifier: CC-BY-SA-4.0
+-->
+
+# Notification-backlog triage — 2026-09-26
+
+Request: clear the [GitHub notifications][notif] backlog — finish chores,
+close issues, resolve unmergeable PRs, and split huge PRs into mergeable,
+comprehensible pieces.
+
+Caveat first: the Arena bot token cannot read the personal
+`/notifications` page (API: `403 Resource not accessible by
+integration`), so this triage reconstructs the backlog from public repo
+state instead: all open PRs/issues on the fork
+(`hyperpolymath/MetaManifold-WebUI`) and the parent
+(`JoshuaJewell/MetaManifold-WebUI`), plus Actions health. If a
+notification is not covered below, point at it and it gets triaged next.
+
+Note: the owner merged fork PR #75 **during this triage** (09:47 UTC);
+the report was updated to match. Fork open PRs are now **zero**.
+
+## TL;DR
+
+| Item | Verdict |
+|------|---------|
+| Fork PR #73 (338 files, conflicting) | **Closed by this triage** — wrong-base duplicate of parent #7 |
+| Fork PR #75 (71 files, ILR bases) | **Merged by the owner during triage** (09:47 UTC) → fork issue #20 auto-closed. Post-merge verification still owed (below) |
+| Parent PRs #8, #10, #11 (300+ files, conflicting) | **Close them** (owner click — bot has no parent write access; commands in `pr7-split/RUNBOOK.md`). Head branches deleted, real deltas already on fork `main` |
+| Parent PR #7 (319 files, clean) | **Keep.** Split into 14 verified stacks: `pr7-split/` (`STACKS.md`, `RUNBOOK.md`, `make-stacks.sh`) |
+| CI on the fork | **Broken repo-wide since 2026-09-25 22:19 UTC** — every file-based workflow `startup_failure`s with zero jobs, including the #75 merge commit. Settings/platform-side; owner action required (runbook appendix 2) |
+| Fork issues (12 open; #20 closed by the #75 merge) | **All remaining stay open** — verified one by one (epic gate, recorded deferrals). Closing any of them now would contradict recorded owner decisions |
+| Branch `arena/01a0db67` (no PR) | **Deleted at owner's request** — content preserved in `docs/triage/db67-rescue/` (stale docs branch, not DOI-deleting — see report) |
+| Parent issue #12 (owner memo) | Awaits the addressee's eyes; summarised below, not closed |
+| Dependabot Updates on fork `main` | **Two consecutive failures** (`36210545146`, `36233872771`); re-run once CI is fixed |
+
+## Actions taken by this triage
+
+1. **Closed fork PR #73** with an explanatory comment ([comment][c73]):
+   same head branch (`feat/stipple-typed-studies-ui` @ `eab8ea0`) is open
+   upstream as parent #7 where it is CLEAN; the fork-side PR rendered as
+   338-file / +65k whole-tree noise after the fork's `git-filter-repo`
+   rewrite severed the merge base back to the initial commit, and was
+   CONFLICTING. Branch untouched; nothing lost.
+2. Recovered the three **deleted head commits** of parent PRs #8/#10/#11
+   by SHA from the fork (`f451f1c0`, `c0be9516`, `b46aee09`) and proved
+   their content is already on fork `main` (`git cherry` patch-identical:
+   `6c29b53b`, ancestor, `0ef5eee`). Wrote the close comments + commands
+   for the owner (bot is `403` on the parent).
+3. Built the **parent-#7 split kit** (`docs/triage/pr7-split/`): 14
+   disjoint stacks covering all 319 files, verified to reproduce the
+   branch tree byte-for-byte, with per-stack review guide and runbook.
+4. Diagnosed the **CI outage** (evidence below) to a settings/platform
+   cause with owner fix steps.
+5. Audited all open fork issues against merged work: #20 closed by the
+   #75 merge; none of the rest qualifies for closure (details below).
+6. Merged the #75 merge commit into this branch, resolving the one
+   `.gitignore` clash (kept both sides: `docs/formal/` + `docs/triage/`).
+
+## The huge PRs, explained
+
+All four 300+ file PRs are the same disease with different prognoses.
+On ~2026-09-24/25 fork `main` was rewritten with `git-filter-repo`
+(~260 MiB of dead blobs stripped; HEAD tree byte-identical — see the
+parent #7 description). The rewrite severed every merge base back to the
+initial commit, so any branch diffed against the "wrong" base renders as
+a whole-tree diff:
+
+- **Parent #7** (319 files, +22,662/−404): branch is `upstream/main` + 3
+  commits, so the diff is REAL and the PR is CLEAN. Genuinely large →
+  split kit provided.
+- **Fork #73** (338 files, +65,571/−22): same branch against rewritten
+  fork `main` → noise + conflicts → closed as duplicate.
+- **Parent #8/#10/#11** (~315–345 files, ~+60k): branches cut from
+  fork `main`, PR'd at upstream `main` (July snapshot) → noise; real
+  deltas were 2/0/1 commits, all now on fork `main`; branches deleted
+  → close.
+
+## Fork PR #75 — merged during triage (verification owed)
+
+`feat(analysis): PhILR, SBP and balance-dendrogram ILR bases`
+(`e2adbb9`, 71 files, +6,918/−78) was merged by the owner at 09:47 UTC
+with CI `startup_failure` and CodeFactor FAILURE — i.e. the PR's own
+"Closes #20 once CI is green" condition was bypassed, and fork issue
+#20 auto-closed. That is the owner's call to make; the owed follow-up:
+
+1. Once CI runs again, confirm the `CI` + `DOI publication contracts`
+   lanes pass on the merge commit — the PR author never executed Julia
+   in their sandbox, so CI is the first real execution of the new tests,
+   reference implementation and benchmarks.
+2. Check whether the CodeFactor FAILURE flagged anything actionable in
+   the merged code.
+3. Re-run Dependabot Updates (failed twice on `main`).
+
+## CI outage — evidence
+
+- Since 2026-09-25 22:19 UTC, **100% of file-based workflow runs** end
+  `startup_failure` with **zero jobs**: `CI`, `DOI publication
+  contracts`, `Stipple UI contracts` — on `main` pushes, PRs, bot and
+  Dependabot actors alike (e.g. runs `36210930780`, `36210537997`,
+  `36196688881`, and the #75 merge runs `36233864893`/`36233864472`).
+- The break is **not the workflow files**: `ui.yml` last ran green on
+  2026-09-21, is unchanged since, and fails identically now. All
+  workflows report `active`. Before 22:19 the same files executed jobs
+  (red, but running).
+- Dynamic (non-file) workflows still run: CodeQL succeeds on the same
+  commits; Dependabot Updates jobs execute (and fail on their own
+  merits).
+- A previous session saw the UI banner: *"Actor is not allowed to
+  trigger Actions workflows"*; `gh run rerun` is refused
+  ("workflow file may be broken" — GitHub's stock message for
+  un-rerunnable startup failures).
+- A sibling probe branch (`arena/01a0db23`, "probe whether file-based
+  workflows can start here") also startup-fails.
+
+Conclusion: settings- or platform-side block on starting file-based
+workflows. Owner steps: read the exact banner on any failed run,
+check Settings → Actions → General on both repos, push a no-op commit
+from a human account to discriminate actor-block vs global break, and
+escalate to GitHub Support if humans fail too. Full steps in
+`pr7-split/RUNBOOK.md` appendix 2. **Everything merge-gated waits on
+this**: any #7 stack PRs, Dependabot, and post-merge verification of #75.
+
+## Issues — why the remaining 12 stay open
+
+| # | Issue | Why it stays open |
+|---|-------|-------------------|
+| 1 | Validated Julia statistics layer (epic) | 14-item acceptance gate ending in *independent review + explicit owner approval*; the issue text says closing it administratively does not open the symbolic gate |
+| 2 | BLOCKED symbolic-engine gate | Blocked by #1 by recorded owner decision; it is the gate, not work |
+| 3 | Exact statistics (Fisher/exact-NB/permutation) | Recorded owner *decision* to defer (catalogue item 4, excluded from v1); code shows only refusal/doc mentions |
+| 4 | Symbolic engine for formulae | Deferred; gated by #1/#2 |
+| 5 | ANCOM-BC / ALDEx2 / Songbird | Deferred; no implementation merged |
+| 6 | CladeCumulus phylogenetic integration | Deferred; `clade_cumulus.jl` exists on the PR branch, not merged |
+| 7 | Full Evidence Mode | Deferred; PR #74 added only a minimal DOI publication page + launcher |
+| 8 | Zenodo integration | PR #74 says explicitly "No issue is being closed by this PR" — needs live sandbox acceptance + baselines first |
+| 17 | Multinomial / Dirichlet-Multinomial | Deferred roadmap item, no PR |
+| 18 | Occupancy / ZINB / hurdle models | Deferred roadmap item, no PR |
+| 19 | Constrained ordinations | Deferred roadmap item, no PR |
+| 21 | Advanced zero handling | Deferred roadmap item, no PR (PR #75 shares Agda groundwork with it) |
+
+Closed during this triage: **#20** (by the #75 merge). Previously
+closed issues (#9–#16, e.g. #9 AnalysisConfig v1) stay closed.
+
+## Flag (resolved): branch `arena/01a0db67-metamanifold-webui`
+
+**Update: deleted on 2026-09-26 at the owner's request; content preserved
+in `docs/triage/db67-rescue/`** (`deleted-branch.patch` recreates the
+branch tree byte-for-byte; restore commands in that directory's
+`README.md`). Branch head at deletion: `d94ecd4e99dbda819fdc0fe1913d5caaabca414a`.
+
+Correction to the first triage note: this branch did **not** actively
+delete the DOI subsystem. It was three docs commits on the pre-DOI base
+`e33e10f`, so diffed against current `main` it merely *appeared* to
+delete `src/doi/*` and the ILR work (base-difference noise — a GitHub
+3-way merge would not have reverted PR #74/#75). Its genuine content was
+a BerryWiki wiki (`docs/wikis/`, 33 pages), `README.adoc`/`EXPLAINME.adoc`,
+the autolink spec, and prose updates to `CHANGELOG`/`CONTRIBUTING`/`NOTICE`
+— plus a `README.md` deletion and 32 wiki pages missing SPDX headers,
+which were the real landmines and the reason for closing it.
+
+Also already gone: the merged PR #75 branch (`arena/01a0db2e`) was
+auto-deleted on merge. Still open and deliberately untouched: the CI
+probe branch `arena/01a0db23` (unmerged, no PR — needs its own decision)
+and `feat/stipple-typed-studies-ui` (live as parent PR #7).
+
+## Parent issue #12 (owner memo, 0 comments)
+
+"Notice to Project Owner: Comprehensive Review & Roadmap Status
+(2026-09-25)" — a long plain-English memo addressed to the project
+owner explaining the fork's work (fake-number removal, real models,
+refuse-to-guess, the four parent PRs). It is FYI, not actionable, and
+needs the *addressee's* eyes before closing — left open deliberately.
+
+## Suggested order of operations for the owner
+
+1. Fix CI (runbook appendix 2) — unblocks everything.
+2. Close parent #8/#10/#11 (one command each, runbook appendix 1).
+3. Decide parent #7: Option A merge-as-is (review via `STACKS.md`) or
+   Option B stacked PRs (`RUNBOOK.md`).
+4. ~~Decide `arena/01a0db67`~~ — done: branch deleted, content preserved
+   in `docs/triage/db67-rescue/`. Remaining: decide the CI probe branch
+   `arena/01a0db23` (unmerged, no PR).
+5. Read parent #12, then close it.
+6. Post-merge verification of #75 once CI runs (Julia tests, CodeFactor
+   findings, Dependabot re-run).
+
+[notif]: https://github.com/notifications
+[c73]: https://github.com/hyperpolymath/MetaManifold-WebUI/pull/73#issuecomment-5845153601
+[p7]: https://github.com/JoshuaJewell/MetaManifold-WebUI/pull/7
+
+## Sweep 2 (same day, ~10:30 UTC) — leftovers the bot could still clear
+
+1. **Kit PR #76: MERGEABLE**, CodeQL + CodeFactor green, semgrep pending.
+   No CI/DOI checks report (outage). Ready whenever the owner is.
+2. **CodeFactor on the #75 merge: 3 × "Complex Method" notices, style
+   only** — `IlrBasisInputs.tsx:39`, `analysis_config.ts:143`,
+   `AnalysisConfigEditor.tsx:21` (run `108381688702`). Not correctness
+   blockers: refactor-or-accept during post-merge verification.
+3. **Dependabot: API rerun refused too** ("cannot be rerun" stock
+   message), so both `main` failures wait on an owner UI re-run or the
+   next Dependabot cycle after CI is fixed.
+4. **Probe branch `arena/01a0db23`: KEEP — do not delete.** True delta is
+   14 files, +2,896/−2, all additive, SPDX-clean: the issue-#21 Agda
+   proofs + `golden.json` fixture, the KYAML pilot (`KYAML.jl`, gate,
+   docs), and the spent CI probe. Landing notes for whoever opens its
+   PR: `proofs/agda/README.md` will add/add-conflict with #75's copy
+   (merge contents by hand); `test/runtests.jl` needs the one-line
+   kyaml include re-applied next to #75's; `*.agdai` would duplicate
+   (harmless, tidy it); drop `ci-probe.yml` (probe answered); note its
+   `EXPLAINME.adoc` differs from the db67 copy archived in
+   `docs/triage/db67-rescue/`.
+5. **Parent #12: §4 walkthrough + §5 Option B are now stale** — they
+   describe #8/#10/#11 as small reviewable PRs, but those have deleted
+   branches and render as whole-tree noise. Draft correction for the
+   owner to paste as a comment (bot is 403 on the parent):
+
+   > Correction (26 Sept triage): PRs #8, #10 and #11 no longer have
+   > live branches and cannot be reviewed or merged as §4 describes —
+   > their real changes (2/0/1 commits) are already on the fork's
+   > `main`, so they should be closed, not reviewed. Please review #7
+   > instead (a 14-part review guide now exists on the fork at
+   > `docs/triage/pr7-split/STACKS.md`). §5 Option B is therefore
+   > obsolete; options A, C and D stand as written.
@@ -0,0 +1,54 @@
+<!--
+SPDX-License-Identifier: CC-BY-SA-4.0
+-->
+
+# Deleted branch `arena/01a0db67` — content preserved here
+
+On 2026-09-26 the owner asked for this branch to be **closed (deleted)**
+during the notification-backlog triage. Before deletion its full content
+was preserved in this directory so nothing is lost:
+
+- `deleted-branch.patch` (260 KB): the branch's true delta
+  (`e33e10f..d94ecd4`, 41 files, +4,138/−691), verified to recreate the
+  branch tree byte-for-byte.
+- `deleted-branch-files.txt`: the file list (`A`/`M`/`D` per file).
+
+## What the branch was
+
+Three docs commits on top of `e33e10f` (fork `main` before the DOI and
+ILR merges): a BerryWiki-format wiki (`docs/wikis/`, 33 pages),
+`README.adoc` + `EXPLAINME.adoc`, the autolink specification
+(`docs/integration/autolink-references.md`), a `.gitignore` negation for
+`docs/wikis/`, and prose updates to `CHANGELOG.md`, `CONTRIBUTING.md`
+and `NOTICE` (third-party table + acknowledgements). It also deleted
+`README.md`, intending the `.adoc` pair to replace it.
+
+## Correction to the first triage note
+
+The first version of this triage's report called this branch
+"DOI-deleting". That overstated it: diffed against *current* `main` the
+branch *appears* to delete `src/doi/*` and the ILR work, but that is
+base-difference noise — the branch predates those merges
+(`git-filter-repo` era base `e33e10f`), so it never contained them. A
+GitHub 3-way merge would **not** have reverted PR #74/#75. The genuine
+landmines were the `README.md` deletion and the 32 wiki pages missing
+SPDX headers (which would fail `scripts/check-spdx.sh`).
+
+## Restore (if ever wanted)
+
+```sh
+git fetch https://github.com/hyperpolymath/MetaManifold-WebUI.git \
+  arena/01a0dd12-metamanifold-webui
+git checkout FETCH_HEAD -- docs/triage/db67-rescue
+git checkout -b restore/db67 e33e10f
+git apply --index docs/triage/db67-rescue/deleted-branch.patch
+git commit -m "restore: db67 docs branch content"
+```
+
+Before merging a restore: rebase onto current `main`, decide
+`README.md` vs `README.adoc` (keep both until decided), and add
+`SPDX-License-Identifier: CC-BY-SA-4.0` headers to the wiki pages
+(the `_Sidebar.md` file is generated upstream — its header needs to
+come from the generator, or the file needs a gate exemption).
+
+Branch head SHA at deletion: `d94ecd4e99dbda819fdc0fe1913d5caaabca414a`.
@@ -0,0 +1,41 @@
+M	.gitignore
+M	CHANGELOG.md
+M	CONTRIBUTING.md
+A	EXPLAINME.adoc
+M	NOTICE
+A	README.adoc
+D	README.md
+A	docs/integration/autolink-references.md
+A	docs/wikis/Deep-Dives--Advanced-Functionality.md
+A	docs/wikis/Deep-Dives--Compositional-Statistics.md
+A	docs/wikis/Deep-Dives--Design-Progression.md
+A	docs/wikis/Deep-Dives--Epistemic-Status.md
+A	docs/wikis/Deep-Dives--Exact-Arithmetic.md
+A	docs/wikis/Deep-Dives--Maximum-Likelihood.md
+A	docs/wikis/Deep-Dives--Type-Theory-Meets-Statistics.md
+A	docs/wikis/Deep-Dives.md
+A	docs/wikis/Developers--Architecture-Tour.md
+A	docs/wikis/Developers--Extending-the-Pipeline.md
+A	docs/wikis/Developers--REST-API.md
+A	docs/wikis/Developers--Statistics-Internals.md
+A	docs/wikis/Developers--Testing-and-Benchmarks.md
+A	docs/wikis/Developers--Type-System.md
+A	docs/wikis/Developers.md
+A	docs/wikis/Home.md
+A	docs/wikis/Maintainers--Compliance-and-Estate.md
+A	docs/wikis/Maintainers--Operator-Track.md
+A	docs/wikis/Maintainers--Releases-and-Distribution.md
+A	docs/wikis/Maintainers--Steward-Track.md
+A	docs/wikis/Maintainers.md
+A	docs/wikis/README.md
+A	docs/wikis/Status-and-Roadmap.md
+A	docs/wikis/Users--Analysis-and-Statistics-Today.md
+A	docs/wikis/Users--Configuration-Reference.md
+A	docs/wikis/Users--Exploring-Results.md
+A	docs/wikis/Users--For-Academics.md
+A	docs/wikis/Users--For-Lab-Professionals.md
+A	docs/wikis/Users--Install-and-First-Run.md
+A	docs/wikis/Users--Troubleshooting.md
+A	docs/wikis/Users--Your-First-Study.md
+A	docs/wikis/Users.md
+A	docs/wikis/_Sidebar.md