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fix(analysis): load CompositionalModels and include clade_cumulus once - #277
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hyperpolymath wants to merge 2 commits into
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main cannot load. src/analysis/differential.jl:36 imports CompositionalFit,
CompositionalRefusal and RuntimeRefusal from ..CompositionalModels, and
src/analysis/compositional.jl defines that module, but src/MetaManifold.jl never
included it, so the package dies with
UndefVarError: `CompositionalModels` not defined in `MetaManifold`
at differential.jl:38 before any test runs (CI run 39873811778). The module is
now included before differential.jl. It has no dependencies of its own, so it
needs no other ordering constraint, and every name differential.jl imports from
it is exported.
clade_cumulus.jl was included twice in the same block, which redefines a module
rather than reusing it; Julia warns 'replacing module CladeCumulus' and re-runs
every top-level definition. One include, in the same position, is enough.
Not changed: src/server/routes/cladistics.jl exists but is not included by
src/server/server.jl, so its /api/v1/studies/{study}/cladistics endpoints are
unreachable. Wiring it adds new routes, which is a behaviour change rather than
a load fix, so it is left for whoever owns that feature.
Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>
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hyperpolymath
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Closed as superseded, not merged. This is a measurement, not a judgement about the work.
The load fix it proposes is already on
Nothing is lost by closing this. A closed pull request keeps its head reachable at The branch itself is deleted because 13 heads of the same shape are what made a fresh pull request impossible to pick out of the list. Background and the classification rules: docs/maintenance/repository-hygiene.md. Reopen this pull request, or open a new one from the current tip, if any of the commits above still applies. |
auto-merge was automatically disabled
October 25, 2026 08:44
Pull request was closed
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hyperpolymath
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Oct 25, 2026
…les (#285) ## Change and reason `main`'s remote held **fifteen heads**: `main`, the orphan data branch the badge publisher force-pushes, and **thirteen branches cut from snapshots between 5 and 119 commits old** — every one of them carrying an open pull request. Six required contexts (`Julia tests`, `Agda proofs`, `Code relevance`, `Occupancy relevance`, `Occupancy disagreement test`, `Occupancy typed peak`) mean a branch in that state reports `BLOCKED` indefinitely, so a reviewer saw thirteen blocked pull requests and no signal about which of them was alive. Each also started a full CI run that could never go green, which is the mechanism that made the pile stable rather than self-correcting. `CONTRIBUTING.md` already required a branch to start at the tip of `main` (rule 1) and to carry no merge commits from it (rule 2). Nothing enforced either sentence. This PR adds the enforcement, the measurement, and the record — and nothing that deletes anything: | Path | What it is | | --- | --- | | `scripts/maintenance/check-pr-freshness.sh` | Answers rules 1 and 2 from the merge base and the commit graph. Annotates the failure for the checks API. Exits 2 rather than passing when it cannot judge. | | `scripts/maintenance/triage-branches.sh` | Classes every remote head as `base`, `unrelated`, `contained`, `fresh`, `salvage` or `stale`. Read-only: `--format table\|markdown\|json`, `--fail-on`. | | `.github/workflows/pr-freshness.yml` | Runs the freshness check on pull request open, push, reopen and ready-for-review. | | `.github/workflows/branch-hygiene.yml` | Weekly: runs the triage into **one** rolling issue that updates in place and closes itself when no drifted branch remains. A job that opens an issue every week is the mechanism that produced the pile it is meant to clear. | | `scripts/tests/test-*.sh` | Fixture-repository tests for both scripts: merged, drifted-with-nothing-new, drifted-with-a-file-the-base-lacks, orphan, unrelated history, shallow, and the Actions annotation path. Wired into the `Advisory scan contract` job beside the other shell tests. | | `docs/maintenance/repository-hygiene.md` | The classes, what happens to each, the recovery path, the 2026-10-25 measurement, the order the work was done in, and the four decisions left to the owner. | | `CONTRIBUTING.md`, `.gitignore` | Points at the doc above; `!docs/maintenance/` follows the existing whitelist pattern (`docs/*` is ignored except published notes). | Two things both scripts refuse to do, because a wrong answer is worse than none: report on a **shallow clone** (it reports its graft point as the merge base, which makes every branch look `fresh`), and delete anything. `governance-badges` is classed `unrelated` and left alone — it is an output, not a spare branch: `README.md` reads it through `img.shields.io/endpoint`. ## Work already done on the remote with these scripts The cleanup is not in this diff, because it is not a file change. Measured, then closed, then the branch deleted — in that order, so each pull request keeps its head reachable at `refs/pull/<n>/head`: - **contained** (`ahead` 0, nothing to merge): #283, #281. - **stale** (behind, adds no file `main` lacks): #284, #280, #279, #278, #274. - **fresh but a duplicate**: #277 — its load fix is already on `main`, and it arrived through a merge commit, which rule 2 forbids. - **salvage** (behind, holds files `main` lacks — closed, not merged, because a merge would revert the 119 commits in between): #276 (Full Evidence Mode, parked by the absorption register per #7), #272, #270, #269 (placement-LWR `ComputingNote.tsx` + threshold test), #271 (evidence-27 review docs). Every close comment carries its own branch's numbers and the `git fetch origin pull/<n>/head` recovery command. The remote is now `main` + `governance-badges`; `triage-branches.sh` reports 2 heads, 0 stale. ## Validation Run here, on this branch: ``` bash scripts/tests/test-triage-branches.sh # 13 passed, 0 failed bash scripts/tests/test-check-pr-freshness.sh # 11 passed, 0 failed bash scripts/check-governance-contract.sh # 70 checks passed bash scripts/tests/test-governance-contract.sh # all mutations rejected bash scripts/tests/test-scanner-boundaries.sh # ok bash scripts/tests/test-ci-logging.sh # ok bash scripts/ci/check-shell-secrets.sh # no credentials in tree or history bash scripts/lint-sonar-reliability.sh # OK: no S2871 or S7758 in frontend/src bash scripts/maintenance/triage-branches.sh # 2 heads after the cleanup bash scripts/maintenance/check-pr-freshness.sh # OK: at the base tip, no merge commits ``` Both new workflows were parsed as YAML and their embedded shell extracted and checked with `bash -n`; the rolling-issue upsert was exercised against a stub `gh` for all three paths (create, update, close). **Not run:** the Julia suite and the frontend suite — neither is touched by this diff, and neither can run in this sandbox; CI is the first execution of anything in this PR on a runner. ## Scope Deliberately not done, each recorded in `docs/maintenance/repository-hygiene.md` under *Decisions for the owner*: 1. **`Branch freshness` is not a required context yet.** It cannot be: a required check that no workflow produces blocks every pull request, including the one that would add it. Add it to the `Branch-Floor` ruleset after this merges. 2. **Push-run concurrency on `main` is untouched.** `cancel-in-progress: false` for pushes serialises the queue — at the time of measurement the run for `a3a4a8e` was still going and the run for `f3816e5a` had not started 25 minutes later. Changing it trades a per-commit result for latency; that is the owner's call, not a CI fix I should make silently. 3. **The SonarCloud gate is untouched.** It failed on most of those pull requests with `C Security Rating on New Code`, is not a required context, and is already documented in `docs/sonar-quality-gate.md`. It was a symptom of the huge stale diffs, not a defect in this repository. 4. **`docs/milestones/02-deferred-issues.md` is referenced by issue #4 and absent from `main`.** The pre-sync archive had it. Restoring it re-adds content that overlaps `docs/statistics/method-catalogue-v1.md`; editing the issue's reference may be the better answer. No lockfile, dependency, generated or vendored file changes. ## Contribution checks - [x] I followed [CONTRIBUTING.md](../CONTRIBUTING.md). - [x] This branch starts at current upstream main and contains no merges from fork main (`merge base f3816e5` = `main` tip). - [x] CI has run and passes — the branch's first CI run is this pull request. - [x] Existing licensing, citation and acknowledgement text is unchanged. --------- Co-authored-by: Arena Agent <agent@arena.ai> Co-authored-by: arena-agent <297053741+arena-agent@users.noreply.github.com>
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main cannot load. src/analysis/differential.jl:36 imports CompositionalFit, CompositionalRefusal and RuntimeRefusal from ..CompositionalModels, and src/analysis/compositional.jl defines that module, but src/MetaManifold.jl never included it, so the package dies with
at differential.jl:38 before any test runs (CI run 39873811778). The module is now included before differential.jl. It has no dependencies of its own, so it needs no other ordering constraint, and every name differential.jl imports from it is exported.
clade_cumulus.jl was included twice in the same block, which redefines a module rather than reusing it; Julia warns 'replacing module CladeCumulus' and re-runs every top-level definition. One include, in the same position, is enough.
Not changed: src/server/routes/cladistics.jl exists but is not included by src/server/server.jl, so its /api/v1/studies/{study}/cladistics endpoints are unreachable. Wiring it adds new routes, which is a behaviour change rather than a load fix, so it is left for whoever owns that feature.
Change and reason
Validation
Scope
Contribution checks