[hyperpolymath]

What is broken on main

using MetaManifold fails on c978994, so the Julia suite cannot run at all. Two merge artefacts are left over from the compositional-differential work:

File	Fault
src/core/doi.jl	module DOI declared twice (lines 4 and 21). The inner declaration swallows the module body and leaves the outer one without an end, so the file cannot be included.
src/MetaManifold.jl	analysis/clade_cumulus.jl included twice, and analysis/compositional.jl never included. Differential does using ..CompositionalModels, so loading dies with UndefVarError: CompositionalModels not defined.

The routes (#211), the frontend and the unit tests are already correct; this is the remaining piece that keeps the package from loading, plus the documentation the merge dropped.

Changes

• src/core/doi.jl — remove the duplicated module DOI.
• src/MetaManifold.jl — drop the duplicate clade_cumulus include; include analysis/compositional.jl before analysis/differential.jl, with a comment explaining the ordering requirement.
• README.md — restore the ancom_bc, aldex2, songbird, multinomial and dirichlet_multinomial method bullets, the "why a count model", "choosing the reference taxon" and "overdispersion" sections, and the nine-method analysis.differential config block (including mn_reference_taxon, mn_penalty, dm_overdispersion_method, max_iter, tolerance, max_seconds).
• ROADMAP.md, docs/statistics/zero-handling.md — describe the five compositional models and note that the multinomial models replace no zero.

songbird (R) and multinomial (Julia) remain two implementations of the same baseline-category model, both selectable, neither an alias — as documented in src/analysis/differential.jl.

Verification

• ./node_modules/.bin/tsc --noEmit -p . — 0 errors.
• bun test src — 85 pass / 0 fail.
• tree-sitter-julia parse of every src/**/*.jl and test/**/*.jl — clean (same three known parser false positives as before).
• Cross-reference audit: every Differential.x / CompositionalModels.x reference resolves.
• Julia itself is not available in the working environment, so test/runtests.jl runs here in CI for the first time since the merge.

Known, out of scope

src/server/routes/cladistics.jl is not included by src/server/server.jl, and it calls CladeCumulus.asv_tip_name / CladeCumulus.analyse_phylogeny, which do not exist. Wiring it in as-is would break the server, so it is left untouched; the Cladistics build API needs a follow-up.

[chatgpt-codex-connector]

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• ROADMAP.md
• docs/statistics/zero-handling.md

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[github-actions]

Fork governance

Lane	Status	Run
DEED syntax (repo deed)	🟢 conformant	run 39880294701
Hypatia verdict grid	purple (job: success)	same run

🟣 critical · commit a840c5e65a3c · run 39880294701

Reporter	Status	Critical	High	Medium	Minor	Since previous revision
Hypatia scan	🟣 critical	47	63	31	0	↔ unchanged
panic-attack assail	🔴 high	0	6	13	0	↓ regressed (1 more blocking)
pons asinorum	🟡 medium	0	0	10	0	↔ unchanged
rhodibot (RSR compliance)	🟠 indeterminate	0	0	0	0	— indeterminate
panicbot (panic recovery, error handling)	🟠 indeterminate	0	0	0	0	— indeterminate
echidnabot (formal verification: proofs/)	🟠 indeterminate	0	0	0	0	— indeterminate
seambot (integration health: API routes)	🟠 indeterminate	0	0	0	0	— indeterminate
finishingbot (release readiness)	🟠 indeterminate	0	0	0	0	— indeterminate
accessibilitybot (WCAG on the React UI)	🟠 indeterminate	0	0	0	0	— indeterminate
glambot (presentation quality)	🟠 indeterminate	0	0	0	0	— indeterminate
cipherbot	⚪ not applicable	0	0	0	0	↔ unchanged
sustainabot	⚪ not applicable	0	0	0	0	↔ unchanged

Hypatia scan: 141 finding(s)

• critical cicd_rules/banned_language_file — frontend/src/views/run/parseFilterYaml.ts — TypeScript file detected -- banned language
• critical cicd_rules/banned_language_file — frontend/src/figure/encode.ts — TypeScript file detected -- banned language
• critical cicd_rules/banned_language_file — frontend/src/figure/charts.ts — TypeScript file detected -- banned language
• critical cicd_rules/banned_language_file — frontend/src/figure/export.ts — TypeScript file detected -- banned language
• critical cicd_rules/banned_language_file — frontend/src/figure/figure.test.ts — TypeScript file detected -- banned language
• critical cicd_rules/banned_language_file — frontend/src/figure/legend.ts — TypeScript file detected -- banned language
• critical cicd_rules/banned_language_file — frontend/src/figure/types.ts — TypeScript file detected -- banned language
• critical cicd_rules/banned_language_file — frontend/src/utils/download.ts — TypeScript file detected -- banned language
• critical cicd_rules/banned_language_file — frontend/src/utils/text.test.ts — TypeScript file detected -- banned language
• critical cicd_rules/banned_language_file — frontend/src/utils/timeago.ts — TypeScript file detected -- banned language
• critical cicd_rules/banned_language_file — frontend/src/utils/text.ts — TypeScript file detected -- banned language
• critical cicd_rules/banned_language_file — frontend/src/hooks/useUnsavedGuard.ts — TypeScript file detected -- banned language
• critical cicd_rules/banned_language_file — frontend/src/hooks/useApi.test.ts — TypeScript file detected -- banned language
• critical cicd_rules/banned_language_file — frontend/src/hooks/useApi.ts — TypeScript file detected -- banned language
• critical cicd_rules/banned_language_file — frontend/src/hooks/useAnalysis.ts — TypeScript file detected -- banned language
• critical cicd_rules/banned_language_file — frontend/src/hooks/useSSE.ts — TypeScript file detected -- banned language
• critical cicd_rules/banned_language_file — frontend/src/hooks/useTabParam.ts — TypeScript file detected -- banned language
• critical cicd_rules/banned_language_file — frontend/src/hooks/useNavRefresh.ts — TypeScript file detected -- banned language
• critical cicd_rules/banned_language_file — frontend/src/hooks/useJobEvents.ts — TypeScript file detected -- banned language
• critical cicd_rules/banned_language_file — frontend/src/about.ts — TypeScript file detected -- banned language
• 121 more; see the structured report in the artifact.

panic-attack assail: 19 finding(s)

• high DynamicCodeExecution — src/pipeline/dada2/context.jl — eval/Meta.parse in src/pipeline/dada2/context.jl
• high DynamicCodeExecution — src/analysis/analysis.jl — eval/Meta.parse in src/analysis/analysis.jl
• high DynamicCodeExecution — src/analysis/differential.jl — eval/Meta.parse in src/analysis/differential.jl
• high DynamicCodeExecution — src/core/provenance.jl — eval/Meta.parse in src/core/provenance.jl
• high DynamicCodeExecution — scripts/check-julia-syntax.jl — eval/Meta.parse in scripts/check-julia-syntax.jl
• high DynamicCodeExecution — test/unit/test_permanova.jl — eval/Meta.parse in test/unit/test_permanova.jl
• medium UnsafeFFI — src/core/memory_probe.jl — 3 ccall/FFI calls in src/core/memory_probe.jl
• medium InputBoundary — src/server/routes/runs.jl — 2 JSON3.read/JSON.parse call(s) with 0 try block(s) in src/server/routes/runs.jl — these throw on malformed input; wrap in try/catch
• medium InputBoundary — src/server/routes/composition.jl — 6 JSON3.read/JSON.parse call(s) with 2 try block(s) in src/server/routes/composition.jl — these throw on malformed input; wrap in try/catch
• medium InputBoundary — src/server/routes/studies.jl — 4 JSON3.read/JSON.parse call(s) with 2 try block(s) in src/server/routes/studies.jl — these throw on malformed input; wrap in try/catch
• medium InputBoundary — src/server/routes/analysis.jl — 9 JSON3.read/JSON.parse call(s) with 3 try block(s) in src/server/routes/analysis.jl — these throw on malformed input; wrap in try/catch
• medium UnsafeFFI — install.jl — 1 ccall/FFI calls in install.jl
• medium ProofDrift — test/unit/test_occupancy_grade.jl — 2 `@test x isa Y` assertion(s) with no value check — type-only tests may substitute for an unwritten formal theorem in test/unit/test_occupancy_grade.jl
• medium ProofDrift — test/unit/test_evidence.jl — 1 `@test x isa Y` assertion(s) with no value check — type-only tests may substitute for an unwritten formal theorem in test/unit/test_evidence.jl
• medium InputBoundary — bench/advanced_zero_handling/benchmark.jl — 1 JSON3.read/JSON.parse call(s) with 0 try block(s) in bench/advanced_zero_handling/benchmark.jl — these throw on malformed input; wrap in try/catch
• medium InputBoundary — frontend/src/figure/charts.ts — 1 JSON.parse call(s) with 0 try block(s) in frontend/src/figure/charts.ts — JSON.parse throws SyntaxError on malformed input; wrap in try-catch
• medium InputBoundary — frontend/src/tree/model.ts — 1 JSON.parse call(s) with 0 try block(s) in frontend/src/tree/model.ts — JSON.parse throws SyntaxError on malformed input; wrap in try-catch
• medium InputBoundary — frontend/src/api/events.ts — 2 JSON.parse call(s) with 0 try block(s) in frontend/src/api/events.ts — JSON.parse throws SyntaxError on malformed input; wrap in try-catch
• medium InputBoundary — frontend/src/components/alphaMetrics.tsx — 1 JSON.parse call(s) with 0 try block(s) in frontend/src/components/alphaMetrics.tsx — JSON.parse throws SyntaxError on malformed input; wrap in try-catch

pons asinorum: 10 finding(s)

• medium string-concat-in-loop — ./frontend/src/tree/model.ts:122 — string built by repeated concatenation in a loop (T0, HEURISTIC)
• medium string-concat-in-loop — ./frontend/src/tree/model.ts:118 — string built by repeated concatenation in a loop (T0, HEURISTIC)
• medium string-concat-in-loop — ./frontend/src/tree/TreeShapes.tsx:69 — string built by repeated concatenation in a loop (T0, HEURISTIC)
• medium string-concat-in-loop — ./frontend/src/tree/TreeShapes.tsx:66 — string built by repeated concatenation in a loop (T0, HEURISTIC)
• medium string-concat-in-loop — ./frontend/src/tree/TreeShapes.tsx:61 — string built by repeated concatenation in a loop (T0, HEURISTIC)
• medium string-concat-in-loop — ./frontend/src/tree/TreeShapes.tsx:53 — string built by repeated concatenation in a loop (T0, HEURISTIC)
• medium string-concat-in-loop — ./frontend/src/tree/TreeShapes.tsx:43 — string built by repeated concatenation in a loop (T0, HEURISTIC)
• medium string-concat-in-loop — ./frontend/src/tree/TreeShapes.tsx:42 — string built by repeated concatenation in a loop (T0, HEURISTIC)
• medium unreachable-after-jump — ./frontend/src/figure/PaneEditor.tsx:45 — statement is unreachable after an unconditional jump (T0, HEURISTIC)
• medium unreachable-after-jump — ./frontend/src/components/PublicationTablesPanel.tsx:208 — statement is unreachable after an unconditional jump (T0, HEURISTIC)

rhodibot (RSR compliance): not_run — enrolled, but no report-back was received

• 🟠 indeterminate: enrolled, but no report-back was received

panicbot (panic recovery, error handling): not_run — enrolled, but no report-back was received

• 🟠 indeterminate: enrolled, but no report-back was received

echidnabot (formal verification: proofs/): not_run — enrolled, but no report-back was received

• 🟠 indeterminate: enrolled, but no report-back was received

seambot (integration health: API routes): not_run — enrolled, but no report-back was received

• 🟠 indeterminate: enrolled, but no report-back was received

finishingbot (release readiness): not_run — enrolled, but no report-back was received

• 🟠 indeterminate: enrolled, but no report-back was received

accessibilitybot (WCAG on the React UI): not_run — enrolled, but no report-back was received

• 🟠 indeterminate: enrolled, but no report-back was received

glambot (presentation quality): not_run — enrolled, but no report-back was received

• 🟠 indeterminate: enrolled, but no report-back was received

cipherbot: not_applicable — no cryptography is implemented in this repository

• ⚪ not applicable: no cryptography is implemented in this repository

sustainabot: not_applicable — fleet adapter slot reserved; no adapter exists yet (gitbot-fleet README)

• ⚪ not applicable: fleet adapter slot reserved; no adapter exists yet (gitbot-fleet README)

Scope: static findings reported by each row's tool at the named commit. Purple, red, yellow and blue grade the worst finding present; orange is evidence missing, malformed or a scanner that did not run; grey is an explicit scope exclusion with its reason. No row is a security certification. report.json, badge.json and the raw findings are in the verdict-grid artifact on the linked run.

[sonarqubecloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud