Automated lint run. Full scan of all wiki pages for structural integrity, broken references, missing pages, and coverage gaps.
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Executive Summary
The wiki has strong structural foundations with 1,426 source documents and complete schema compliance in sampled pages. However, significant gaps exist in content coverage, index accuracy, and intervention linking.
By the numbers:
- 15 signature pages exist; 14 additional diseases listed in index have no signature page yet
- 13 intervention pages exist; 24 intervention IDs referenced in signatures have no backing file
- 2 STOP IDs referenced in signatures have no backing file
- 7 intervention files exist but are not referenced in any signature
- index.md counts are incorrect across multiple sections
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Critical Issues (Blocking)
1. Missing STOP Pages (2)
These are referenced in signature `stops:` arrays but the files don't exist:
| Referenced ID | Referenced From |
|---|---|
| `stop-diagnostic-overclaiming-discovery-phase` | pancreatic-cancer.md |
| `stop-excess-iodine-supplementation-hashimotos` | hashimotos-thyroiditis.md |
2. Missing Intervention Pages (24)
These are referenced in signature `validated_interventions:` arrays but the files don't exist:
| Missing Intervention | Referenced From |
|---|---|
| acarbose-fiber-synergy | — |
| aip-diet-hashimotos | hashimotos-thyroiditis.md |
| berberine-methimazole | — |
| citrus-fruits | — |
| dietary-fiber | — |
| faecalibacterium-restoration | — |
| ferrichrome-probiotics | — |
| hbot | — |
| high-fiber-diet | — |
| high-fiber-prebiotics | — |
| lactoferrin-supplementation | — |
| low-carbohydrate-diet | — |
| low-fat-diet | — |
| low-red-meat-diet | — |
| magnesium-supplementation | — |
| nac-supplementation | — |
| prebiotics-inulin-fructo-oligosaccharide | — |
| probiotics-lactobacillus-bifidobacterium | — |
| probiotics-thyroid | hashimotos-thyroiditis.md |
| quercetin | — |
| saccharomyces-boulardii | — |
| selenium-supplementation-200mcg | hashimotos-thyroiditis.md |
| synbiotics-pdac | pancreatic-cancer.md |
| vitamin-d-probiotic-synergy | — |
3. Incomplete Frontmatter in depression.md
`wiki/signatures/depression.md` is missing the `validated_interventions` and `stops` frontmatter fields entirely. All other signature files have these fields (some as empty arrays `[]`, which is acceptable). This file needs both fields added.
4. index.md Counts Are Wrong
The index claims incorrect numbers across several sections:
| Section | index.md claims | Actual count |
|---|---|---|
| Disease Signatures | 14 | 15 |
| Interventions | 5 | 13 |
| STOPs | 12 listed | 11 files |
Additionally, these 3 signature pages are missing from the Disease Signatures section in index.md:
- graves-disease
- hashimotos-thyroiditis
- pancreatic-cancer
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High Severity Issues
5. Signatures With No Linked Interventions (8 of 15)
These signatures have empty `validated_interventions: []` arrays, meaning Cureva has no intervention output for these diseases:
- alzheimers-disease.md
- autism-spectrum-disorder-microbiome-signature.md
- cardiovascular-disease.md
- colorectal-cancer.md
- depression.md (also missing the field entirely)
- obesity.md
- parkinsons-disease.md
- type-2-diabetes.md
6. Signatures With No Linked STOPs (same 8)
Same signatures above also have empty `stops: []` arrays.
7. Orphaned Intervention Files (7)
These intervention files exist but are not referenced in any signature's `validated_interventions` array:
- fmt-intervention.md
- iron-management.md
- ketogenic-diet.md (signatures reference `ketogenic-diet-ms` — is this a duplicate or separate?)
- probiotics-asd-dysbiosis.md (likely should be in autism signature)
- probiotics-general.md
- vitamin-d-supplementation.md
- zinc-supplementation.md
8. Orphaned STOP File (1)
- `stop-iron-supplementation-asd.md` — exists but not linked in any signature's `stops` array. Likely belongs in autism signature.
9. Autism Signature Naming Mismatch
The autism file is named `autism-spectrum-disorder-microbiome-signature.md` — the only signature that doesn't follow the standard `disease-name.md` pattern. The index references it by full name which works, but it's inconsistent with all other signatures. Consider renaming to `autism-spectrum-disorder.md` (or document the deviation).
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Medium Severity Issues
10. Missing Signature Pages (14 diseases listed in index with no signature)
These diseases appear in the index Diseases section but have no corresponding file in `wiki/signatures/`:
| Disease | Raw Papers (approx.) | Priority |
|---|---|---|
| Hashimoto's Thyroiditis | 73 | High — signature partially linked |
| Postpartum Depression | 74 | High — estrobolome focus |
| Rheumatoid Arthritis | — | High — Cu/Zn/Fe signature |
| Breast Cancer | — | Medium |
| Chronic Kidney Disease | — | Medium |
| Gastric Cancer | — | Medium |
| GERD | — | Medium |
| Hypertension | — | Medium |
| IBS | — | Medium |
| Inflammatory Bowel Disease | — | Medium |
| Ovarian Cancer | — | Medium |
| Schizophrenia | — | Medium |
| Type 1 Diabetes | — | Medium |
| Ulcerative Colitis | — | Medium |
11. Entity Pages May Be Missing
Sample check in depression.md found references to `clostridium` and `prevotella` — entity pages for these taxa were not confirmed to exist. A full audit of entity references across all 15 signature pages is needed.
12. ASD Papers Unprocessed
~180 ASD papers are reportedly in a disorganized folder awaiting ingest. The autism signature has `cureva_status: in-progress` and empty intervention/stop arrays, consistent with incomplete processing.
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Triangle Evidence Status
Sampled intervention files (b-cell-depletion-therapy-ms, ecoli-nissle-1917, ketogenic-diet-ms, low-nickel-diet) all contain complete triangle evidence with all required fields:
- `I_to_f` + `I_to_f_evidence`
- `I_to_D` + `I_to_D_evidence`
- `f_to_D`
- `status`
No triangle evidence gaps detected in existing intervention files. ✓
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Recommended Next Steps
Immediate (blocking):
- Fix `depression.md` — add `validated_interventions: []` and `stops: []` frontmatter fields
- Create 2 missing STOP stubs: `stop-diagnostic-overclaiming-discovery-phase`, `stop-excess-iodine-supplementation-hashimotos`
- Update `index.md` — fix counts and add missing signature entries
High priority:
- Reconcile 7 orphaned intervention files — link to signatures or remove
- Link `stop-iron-supplementation-asd` to autism signature
- Build the 3 highest-priority missing signatures: Hashimoto's, Postpartum Depression, Rheumatoid Arthritis
- Create stubs for the 24 missing intervention files (even empty stubs break no links)
Medium priority:
- Audit entity references across all 15 signatures; create missing entity pages
- Process 180 ASD papers; expand autism signature to `cureva_status: partial`
- Resolve autism signature naming inconsistency
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Files Scanned
- `wiki/index.md`
- `wiki/log.md`
- All 15 files in `wiki/signatures/`
- All 13 files in `wiki/interventions/`
- All 11 files in `wiki/stops/`
- Sample of `wiki/sources/` and `wiki/entities/`
- `wiki/analyses/gaps-and-improvements-2026-04-12.md` (prior gap analysis)