Methodology coverage

Temporary planning document; planning only. It answers one question: with SyRF's existing capabilities, does this plan add up to a very high quality systematic review facility for preclinical reviews, and what is added, proposed or deliberately left out. It resolves the round-2 methodology findings (review SR in full; V2-01..04 and V2-10..14; PH-10, PH-12, PH-23, PH-24; review AC-04, AC-20, AC-21; MS-11; DD-08; NS-06). The text it proposes for the package files has been merged into them: PRISMA amendments (preamble, summary, G, H, J, K, L and the new M, N and O), contracts C3, C12 and C14, the integrated plan (R3b, R5b and R5c scope; the P1, P2, O1 and X1 lane rows), acceptance criteria (the release criteria cited below and the §7 PRISMA fixtures) and open questions (E88–E93, A-39, A-40, Q-37); this page explains and justifies.

Labels follow the package: OWNER, RECOVERED, PROPOSAL, OPEN (Q-xx), ASSUMPTION (A-xx), CODE-MAIN, CODE-PR, DOC-APPROVED, DOC-DRAFT. Anything that needs Chris cites a Batch D question ID from the resolution brief; this page mints no question IDs. Methodology sources are named inline: PRISMA 2020 (Page et al. 2021), PRISMA-S (Rethlefsen et al. 2021), Cochrane Handbook v6 (chapter 4 selection, chapter 5 data collection, chapter 6 effect measures, chapter 7 risk of bias), SYRCLE's RoB tool (Hooijmans et al. 2014), the CAMARADES quality checklist (Macleod et al. 2004), ARRIVE 2.0 (Percie du Sert et al. 2020), ASySD (Hair et al. 2023), Vesterinen et al. 2014, and the inter-rater reliability literature (Cohen 1960, Fleiss 1971, Krippendorff 2004, Byrt et al. 1993 for PABAK, Gwet 2008 for AC1). Claims about main were checked against /home/chris/workspace/syrf/main at de3e98c59 (3 October 2026); anything not checked is marked UNVERIFIED.

1. Purpose and status

• Verdict. The package already makes the evidence core sound: immutable revisions, snapshot gold, no fabricated history, as-of reproduction, per-profile collective outcomes as the only PRISMA authority (PR1, amendments A and H). What it lacked, and what review SR showed, is the layer a journal or a funder sees: a defined inter-rater reliability basis, a human full-text retrieval workflow, protocol and search documentation, risk-of-bias templates, extraction provenance and validators, PRISMA arithmetic, report-to-study linkage, analysis-ready exports and calibration. With the additions below the plan does add up to a very high quality facility. Each addition is small relative to the engine work; most are data fields, rules and templates on aggregates the plan already creates.
• What this page decides. Nothing. It restates confirmed owner decisions, adopts review improvements as PROPOSALs, and routes product choices to Batch D (D4-01..D4-21, plus D3-11, D3-12, D3-25, D2-12 and D2-15 where they bear on methodology).
• Status of the PRISMA amendments. A, C, D, G, H, I and J are approved (Q-06a); B, E and F are open (Q-06b); K and L were requested by Chris with rules pending (Q-37). This page adds M (full-text retrieval), N (Citation to Publication link) and O (report-to-study linkage, conditional on D4-08), and restates G, H, J, K and L. The amendment text is in prisma-amendments.md.
• Relation to the other round-2 documents. The IRR markers it proposes live in C3 (contract owner: the consistency drafter writes C18/C19; this page supplies the C3 rows). Version compatibility guards for autoUpdate (SR-16) are decided in versioning-model.md (§1.9 of the brief); this page adds only the export columns that make them visible. Deletion versus history is D3-12; this page records the methodological consequence only.

2. Capability map

Columns: what main does today (verified unless marked), what the package already plans, what this page proposes (with its Batch D ID where Chris decides), and what is deliberately out of scope for this programme.

Area	Today on main	This plan (already in the package)	Proposed here (Batch D)	Out of scope
Protocol and registration	A free-text Protocol Url on the project (user-guide/projects/settings.md:22; Project.cs:37,71 protocolUrl, AddProtocolLink) and free eligibility text. No registration record, no amendment log. CODE-MAIN	Profile versions with publication impact (Q-26) are the de facto criteria history. Amendment F (open, Q-06b) says corrections and protocol amendments append.	A project "Protocol and registration" record: registry, ID, URL, date, protocol document link and version, append-only amendments log; publishing a profile version that changes eligibility requires an amendment entry (D4-05). Methods summary export (§14).	Registry integrations (PROSPERO or OSF lookups); protocol authoring inside SyRF.
Search documentation and rounds	SystematicSearch holds name, description, file type, living-search link and a file-derived study count (SystematicSearch.cs:42-66). No source type, platform, date searched, strategy or limits (FEAT-011 gap G1/G2, prisma-flow-diagram-mapping.md:242-243). Living search exists behind livingSearchConfigurable (env-mapping.yaml:1165-1169); funder status "deferred" (docs/funding/index.md:66). CODE-MAIN	P1 adds sourceType and sourceName (FEAT-011), amendment K external step records, amendment C earliest-source column, withdrawal (J).	PRISMA items 6 and 7 fields on SystematicSearch (date searched, platform, strategy text or file, limits and filters, date range) and a minimal searchRound with updateOf (SR-04, SR-24; D4-05).	Automated search execution, multi-database retrieval, living-search automation (funder "future development").
Deduplication	None in code: "No deduplication tracking at all" (prisma-flow-diagram-mapping.md:244); no pmPublication, no citations[], no lifecycleStatus (no hits in SyRF.ProjectManagement.Core/Model). FEAT-012 is an Approved specification only. DOC-APPROVED	P2 implements FEAT-012 natively (amendment L): two-stage ASySD, tiers, review queue, merge wizard, audit log, retroactive dedup, parity suite.	Merge as an alias, never a re-key (§1.11, DD-08, V2-02; D2-12); QC sample of AutoConfirmed groups; reviewer "flag as possible duplicate"; parity metric (D4-21); Publication privacy and enrichment visibility (V2-03); extended pool exclusion list (V2-12).	Cross-project review-data sharing; tuning the 25 classification rules per project (FEAT-012 §4.2 defers it).
Screening	Binary decisions (ScreeningDecision.cs:3-7: Included=1, Excluded=0); random serving (user-guide/stages/screening.md:28); two independent screeners plus a third by default, single screening configurable and "not recommended" (:73-75); skip via Next (:30); no structured reasons (gap G8, mapping :249); CSV import of decisions mapped to investigators and a stage (user-guide/studies/upload-search.md:38-54). CODE-MAIN	R3a canonical decisions and steps; R3b profiles, derived decisions (DP3), reasons (DP5), own-Exclude correction (DP2), collective outcomes per profile; R4p adjudication; amendments A and H.	Template defaults for new projects (PROPOSAL, §3.1); Unsure at title/abstract (D4-01); discussion route (D4-02); calibration step kind (D4-04); primary-reason hierarchy (D4-13); imported decisions as authority = Imported (SR-03); bibliographic blinding option (SR-25); blinding and random serving as core behaviours (D4-19).	Machine-learning prioritisation or automated exclusion (would populate box 3 excluded_automatic; no lane).
Full-text retrieval	PDFs can be linked or bulk-uploaded; nothing records whether full text was sought or obtained (gap G7, mapping :248). Bulk PDF (FEAT-021) is a separate programme, flag off. CODE-MAIN	P1 "retrieval status recorded with the PDF acquisition and processing programmes" (plan :689); AC-P1-03 events only.	Human actions Sought, Retrieved (how), Not retrieved (reason, author-contact date); PDF attachment only suggests Retrieved; amendment M makes retrieval fullTextStatus only and supersedes FEAT-011's FullTextNotRetrieved lifecycle precedence (SR-02, SR-15; D4-07).	Automated PDF retrieval (funder "future development"); open-access resolvers.
Data extraction	Unit hierarchy (experiment, cohort, disease model, treatment, outcome); average mean/median (export also mode); error SD/SEM/IQR; units as free text; GreaterIsWorse; cohort n (user-guide/data-extraction.md:72-92; data-dictionary/quantitative.md:158-180). Graph digitiser is dead: graph2data flag exists (env-mapping.yaml:1501-1505) but the library import is commented out (src/services/web/src/polyfills.ts:55). CODE-MAIN	O1 schemas (legacy-compatible, event-count, custom) with roles, types, validators and cardinality (C14); reviewer-created measures with one direction (ODIR1); O2 migration; R4c outcome reconciliation.	Extraction-method provenance; unit vocabulary and same-measure unit validator; dispersion catalogue; domain validators; sample-size rule; graph-estimated default when a region is linked (SR-06; D4-10); extract-and-verify (D4-03); extraction QC view (§5.6).	Graph digitiser lane (decided after O1 pilots, D4-10); machine-assisted extraction; effect-size computation.
Risk of bias and reporting quality	Ad hoc annotation questions (seed category "Risk of Bias" with randomisation and blinding items, docs/architecture/seed-data-quality-analysis.md:311); the AI RoB tool is mothballed (docs/roadmap/product-features-roadmap.md:39; docs/features/calculate-rob-authorization.md:66-67); no user-guide page (grep of user-guide/ for SYRCLE or risk of bias: none). CODE-MAIN	R1a question templates; TC1 feature-required entity types; R4a reconciliation gives two-assessor independence for any form.	SYRCLE RoB (per-outcome items bound to Outcome Assessment), CAMARADES checklist, ARRIVE Essential 10 as curated versioned templates with semantic roles, and a domain × study export matrix (SR-05; D4-06, D2-15).	Reviving the AI RoB tool; automated RoB judgements.
Reconciliation and agreement	No reconciler form on main (plan R4a); manual reconciliation via the help desk (screening.md:77); legacy AgreementMeasure getters only; agreement and kappa excluded from FEAT-024 (materialized-project-statistics/README.md:223). CODE-MAIN	R4a form reconciliation and gold (GS1, RE2, VS2 exposure), R4p profile adjudication, R5c agreement view (AG1–AG3; Q-04, Q-16).	Observation basis in C3 (initial independent submission; collective exposure at correction; questioned in reconciliation, NS-06; imported authority); screening IRR per profile; methods for fixed and rotating raters; prevalence shown; drift over time; reconciler-override QC (SR-01, SR-18; D4-12, D3-11).	Automated adjudication; agreement as a FEAT-024 family (D3-11 keeps it in its own store).
Export for synthesis	Long and wide CSV; one row per timepoint per cohort; blinding level on investigator columns; Reconciled flag (quantitative.md:14,30-38). No RIS export, no comparison export, no codebook. CODE-MAIN	R5a current, previous and as-of exports with manifests (C11); export disclosure (C10).	Lane X1: comparison-level export, machine-readable codebook, RIS export (SR-08; D4-09); extraction exports default to collectively Included studies with surplus labelling (SR-17); metaAnalysisIncluded owner and capability (SR-20); goldDiffersFromAllCandidates column (SR-18); version columns (SR-16).	Effect sizes (SMD, NMD), meta-analysis and plots inside SyRF (recipe in the user guide only).
PRISMA reporting	None (no generator; 11 gaps in mapping §5). DOC-APPROVED	P1, P2, R3a/R3b write shapes, R4p, R5b frozen snapshots with manifests; amendments A–L.	Published arithmetic identities per column with remainders (SR-09); entry-phase rule and per-box combination for external steps (V2-04); box 1 from K via D4-11; snapshots from authoritative records only (MS-11); amendments M, N, O; withdrawn searches per D3-12.	Full updated-review support beyond reported box 1 counts; PRISMA-S checklist authoring beyond the methods summary.
Living and updated reviews	Living search feature flagged and funder-deferred; new arrivals re-enter stages (R3c reopening).	R3c automatic reopening for new arrivals; "box 1 stays deferred".	Minimal search rounds (searchRound, updateOf) on searches and external records; per-round identification in R5b; box 1 as reported counts (D4-11).	Automatic re-screening workflows for update searches; previous-review import with PreviouslyIncluded (reserved, FEAT-011 prisma-flow-diagram-mapping.md:264).
Audit and as-of reproducibility	Questions locked after first answer, no versioning (product-features-roadmap.md:37); timestamps settable (DateTimeCreated, C11).	Immutable revisions, versions and snapshots; HLC ordering (§1.2); as-of exports with coverage labels (EX2); frozen PRISMA snapshots; append-only lifecycle, pool-entry and external records.	PRISMA snapshots computed from authoritative records at a watermark, never FEAT-024 rows (MS-11); conversations as audit record only (D3-25); dedup transparency in the manifest.	Selective per-project restore (D2-13 rules it out).
Blinding and independence	Reviewer identities blinded in exports by a level setting (quantitative.md:38); candidates never see each other's screening decisions; random serving.	VS1 candidate isolation, BL1 stage-owned reconciliation blinding with stable aliases (Q-30), VS2 exposure, RA5 blind extra review, export disclosure (U26).	Candidates always blinded, the stage choosing only the alias scheme; random serving default and explicit assignment an audited exception (D4-19); bibliographic blinding per profile (SR-25); discussion exposure recorded (D4-02).	Unblinded "open" reconciliation modes.
Calibration and training	None.	None (QM v2 "training rounds" brief unused, PH-33).	Calibration step kind: a fixed sample offered to every reviewer, records with purpose = calibration that never vote, qualify, enter PRISMA or default IRR; live per-criterion agreement; a passed-training admission hook in C6 (D4-04).	Scored training against gold as an admission prerequisite (after GA; hook reserved).
Quality control	None beyond reconciliation.	R4b queries; R3c readiness; FEAT-024 counts.	Dedup QC sample and reviewer duplicate flag (SR-19); reconciler-override count and column (SR-18); extraction QC view (graph-estimated share, unit mismatches, SD/SEM flips, missing n); methods caveat label for single screening or target-1 extraction (SR improvement 10); near-miss excluded list (PRISMA item 16b).	Statistical outlier detection on extracted values.

3. Screening methodology

3.1 Dual independent screening defaults for new templates

PROPOSAL (SR-21). R3a reproduces the legacy maths for the default profile (inclusion ratio threshold, third vote decides) so adopted projects keep their meaning. New projects deserve an explicit, defensible default, authored as template content by CAMARADES methodologists through the R1a template mechanism (D2-15 for ownership) and recorded as PROPOSAL thresholds at F5:

Template	Target	Decision rule	Conflict route	Reasons	Notes
Title and abstract	2 independent screeners	Unanimity; Unsure allowed (D4-01); Unsure + Unsure → third vote	Blinded third screener (extra vote, D1/D2 Allow)	Optional	Cochrane Handbook ch. 4: "when in doubt, include" at this phase
Full text	2 independent screeners	Unanimity	Adjudication (R4p); discussion off (D4-02)	Required, DP5 On, hierarchy on (D4-13)	PRISMA 2020 item 16b needs a reason per excluded report
Single-screener mode	1	Reviewer's decision stands	None	As configured	Kept (student projects, screening.md:75); sets the methods caveat (§14.3)
Extraction	2 plus reconciliation, or 1 plus verification (D4-03)	RE2 final submission or Verified gold	R4a	n/a	Target-1 unverified is labelled "single extraction, unverified"
Risk of bias	2 plus reconciliation	RE2	R4a	n/a	PRISMA 2020 item 11

A project may change any of these; the methods summary (§14.1) reports what was actually used.

3.2 Unsure at title and abstract (D4-01)

Recommended per profile, default on in the title/abstract template and off in the full-text template. Rules if approved: Unsure routes like Include for downstream availability; the profile's collective rule says how Unsure combines (default: Unsure + Unsure and Include + Unsure need a third vote; Exclude + Unsure is a conflict); a collective Unsure is never Excluded, so PRISMA counts the study as not excluded at title/abstract and it proceeds to retrieval; agreement statistics report Unsure as its own category (three-category κ) and collapsed into Include. DP3 derived decisions may derive Unsure when a criterion answer is "unclear". Today a reviewer who is unsure must Include (contaminating agreement) or skip indefinitely (screening.md:30).

3.3 Discussion route (D4-02)

Recommended per profile, default off. After a conflict both candidates may see each other's decision and reasons; the exposure is recorded in C3 as a collective-exposure event with kind discussion; either may correct through DP2 (a new immutable submission); the profile rules re-run; if the conflict persists the configured route (extra vote or adjudication) applies. IRR uses initial independent observations (§4), so the route never inflates agreement. VS1 is not broken: the exposure is explicit and labelled. Discussion text, where captured through

3944's conversations, is audit record only (D3-25).

3.4 Calibration rounds (D4-04)

Recommended as a step kind, R3c (or after GA with the C6 admission hook reserved now). A fixed sample (admin-chosen or random N; PROPOSAL default 30 studies) is offered to every reviewer regardless of target. Records carry purpose = calibration: they never vote, never qualify a contribution, never create pool-entry or screening events for PRISMA (C12 rule), and are excluded from default IRR, with their own calibration agreement report per criterion. "Promote calibration decisions to live" is an explicit admin action, off by default, that creates new live submissions with provenance; it never relabels. The drift view (§4.6) is the feedback loop Cochrane Handbook ch. 4 asks for when criteria are piloted.

3.5 Primary-reason hierarchy (D4-13)

Recommended: the profile's configured criteria order is the reason hierarchy; a profile rule "primary reason = first failing criterion in configured order" is on by default and can be turned off to let the reviewer choose. The derived decision (DP3) records the primary reason automatically; DP5 reconciliation compares the full set of failing criteria (the R4p view shows each candidate's failing-criteria vector, SR improvement 4); PRISMA reports the primary. Reasons stay countable categories, never free text alone (FEAT-011 prisma-constraint-annotations.md:260-264); when the rule is off and no primary was chosen, the outcome's reason coverage says so (amendment E). This makes box 9 reproducible.

3.6 Imported screening decisions

PROPOSAL (SR-03). Decisions imported from CSV columns (upload-search.md:38-54) or through FEAT-004 (§13.1) are canonical ScreeningDecision records with authority = Imported and provenance: source system, import job, mapped investigator, and independence (unknown, or declared-independent with the declaring admin and time). The import wizard for canonical projects requires the declaration. Declared-independent decisions count toward profile sufficiency and appear in a separately labelled IRR view, never in the default view. Unknown or not-independent decisions are recorded and shown but never count toward sufficiency or IRR. For PRISMA every imported decision counts as "screened in SyRF (imported record)", so amendment K's external counts for the same phase are refused for those records (no double counting). Amendment H's authority list gains Imported. Imported decisions never become gold or adjudicated outcomes automatically.

3.7 Bibliographic blinding

PROPOSAL (SR-25). A per-profile presentation option, default off, hides authors, journal and year during screening; the exposure provenance records that metadata was hidden. Cheap, and some protocols require it to reduce prestige bias.

3.8 Blinding and random serving as core behaviours (D4-19)

The SSI RSMF expression of interest states that blinding of reviewer identities and random study serving are core platform behaviours, not optional settings (docs/funding/ssi-rsmf.md:100). Recommended consequence: candidates are always blinded in reconciliation; BL1 becomes the choice of alias scheme (stable per-project aliases or per-task aliases), never an "off" switch; unmasking goes only through the audited export disclosure contract (C10, U26). Random serving stays the default; explicit assignment (R4a assignment, RA5 requests, allocation plans) is an audited exception. Presence disclosure follows D3-20.

4. Agreement and reliability

4.1 Observation basis

R5c computes agreement "from canonical revisions" but never said which revision per reviewer is the observation (SR-01). Under DP2 a reviewer can correct an Exclude while review is possible, extra votes resolve conflicts, a reviewer can infer the collective state from availability messages, and a reconciler's question may paraphrase other candidates' answers (NS-06). A correction made after any of that is not an independent observation. C3 today records exposure only for accepted gold (contracts.md:163).

PROPOSAL (adopted per brief §1.17 and NS-06): C3 gains four markers, frozen at F1a once D4-12's F1a part is answered:

Marker	Meaning	Written when
Initial independent submission	The first effective Complete (form) or decision (screening) by a reviewer for a (study, form) or (study, profile) context, made before any collective outcome, accepted answer or adjudicator output for that study was visible to that reviewer	Derived at commit from the commit order and the visibility events; stored on the session version
Collective exposure at correction	For DP2 corrections, extra votes and the discussion route: whether the collective outcome (Pending, Conflict, Included, Excluded, Unsure) or any reconciler or adjudicator output was visible to the actor, and through which route (availability, discussion, monitor)	On the correcting submission
Questioned in reconciliation (NS-06)	A reconciler questioned this reviewer's session on this study × form (thread, time); every later version of that reviewer's session on that study × form is informed	By #3965 when a conversation is created, looked up by session; consumed by R5c, C11 manifests and R6 adoption mapping
Imported authority	authority = Imported with independence (§3.6)	At import

Lost or missing markers fail safe: "available but unrecorded" is treated as informed or unknown, never as independent (C3's existing rule). Calibration records (purpose = calibration) are excluded by construction. Conversations themselves are never inputs to agreement; they are audit record, exportable only behind an audit capability with aliases (D3-25).

4.2 Views

Default IRR view = initial independent observations. A current-decision view is available and labelled "current decisions (includes corrections)". Corrections after collective visibility are labelled "informed (collective)"; sessions after a reconciler's question are "informed (questioned)"; declared-independent imported decisions appear in their own view (§3.6). Fixture: a DP2 correction after a visible conflict never changes the initial-observation κ; a questioned reviewer's later version is classified as informed (NS-06).

4.3 Screening IRR per profile

Screening-level agreement is an explicit R5c deliverable (AG1–AG3 and AC-R5c-01 are annotation-answer rules today). Per profile and per phase: percent agreement with explicit denominators (always shown), the prevalence of Include (always shown, because κ is depressed at low inclusion rates typical of title/abstract screening), and:

Rater design	Statistic	Source
Two fixed raters	Cohen's κ (with 95% CI)	Cohen 1960
Three or more fixed raters	Fleiss' κ	Fleiss 1971
Rotating pairs (the SyRF norm: random serving)	Pooled pairwise κ over all rater pairs with ≥ n shared studies, and Krippendorff's α over the incomplete rater × study matrix	Krippendorff 2004
Low prevalence	PABAK and Gwet's AC1 as supplementary, labelled	Byrt et al. 1993; Gwet 2008
Three categories (Unsure)	Three-category κ plus the collapsed binary	§3.2

Per-criterion agreement (which eligibility criterion the raters disagreed on) uses the DP3 failing-criteria vectors. All of this is PROPOSAL pending a statistician's review of denominators (D4-12; Q-16). Until then R5c ships percent agreement with counts, as Q-16 already says.

4.4 Form and entity agreement

Unchanged: AG2 (identical multi-select sets), AG3 (N/A rules, compatible-version flags), Q-04 missing-state contract. Verified gold (D4-03) has no IRR; exports label it "single extraction, verified".

4.5 Reconciler-override QC

PROPOSAL (SR-18). RE1 keeps explanations optional. The R5c view (or R4a's pool page) shows a "reconciler overrides" count: gold differs from every candidate with no explanation, per form and question, exportable; the non-blocking reminder is on by default; exports gain goldDiffersFromAllCandidates.

4.6 Drift over time

PROPOSAL (SR improvement 3). Agreement per reviewer pair and per criterion by screening order (first 100, next 100, …) so drift is visible early; it is the feedback loop for calibration.

4.7 Store

Agreement statistics live in their own rebuildable store, not FEAT-024 (D3-11; MS-20); FEAT-024 excludes kappa (materialized-project-statistics/README.md:223).

5. Data extraction quality

5.1 Extraction-method provenance

PROPOSAL (SR-06a; C14, E12). Every observation carries an extractionMethod role: reported (text or table), graph-estimated, calculated (by the reviewer; the formula noted), author- supplied, unknown. A series-level dataSource note holds the location (table, figure, page). When a PDF graph region is linked, graph-estimated is the default. Cochrane Handbook ch. 5 and Vesterinen et al. 2014 require graph-derived data to be flagged; today the graph link is only a region assignment and the digitiser is dead (polyfills.ts:55).

5.2 Unit vocabulary and the same-measure validator

PROPOSAL (SR-06b). A project unit vocabulary: a controlled list with SI-aware labels and free-text fallback, seeded from a CAMARADES list. A validator "same measure, different unit" warns at Save and blocks binding at reconciliation (R4c) until the reconciler maps or confirms. Today "mm3" and "mm³" are two strings (data-extraction.md:78).

5.3 Dispersion catalogue and the legacy-compatible fields

PROPOSAL (SR-06c), to be fixed before Q-17 closes (E12): average {mean, median, other}; dispersion {SD, SEM, 95% CI lower and upper, IQR Q1 and Q3, range min and max, none reported}; n at observation (default "same as cohort n", with provenance); events and total for dichotomous outcomes (event-count schema); time with unit. Dispersion is never converted on export (the analyst converts; the recipe is in the user guide). This gives "variation" (OC1, Q-17) a definition: the dispersion role and its catalogue value. Legacy IQR and export mode map to catalogue values with a recorded alias (O2 mapping contract, outcome-data migration proposal :95).

5.4 Domain validators

PROPOSAL (SR-06d), enforced on Save (AC-O1-02, AC-O1-11): SD ≥ 0 and SEM ≥ 0; n an integer > 0; events ≤ total; time monotone within a series; CI lower ≤ average ≤ CI upper; Q1 ≤ median ≤ Q3; an SEM/SD plausibility warning when a series mixes types (SEM × √n ≈ SD); a direction never derived from values (OC2). Warnings never block Save; blocking rules block Complete.

5.5 Sample-size rule

PROPOSAL (SR-06e). The analysis n is the observation-level n when recorded, else the cohort n; exports carry both and the rule applied (nSource). O2 never overwrites a cohort count with a series count (migration proposal :96).

5.6 Extraction QC view

PROPOSAL (SR improvement 5), O1 or R4c: per form, the count of graph-estimated observations, unit-mismatch warnings, SD/SEM corrections made at reconciliation and observations with missing n. These are the questions referees ask.

5.7 Graph digitisation (D4-10)

Recommended: ship the provenance flag in O1 now; decide a digitiser lane after O1 pilots report how often a graph is the only source. Until then "graph-estimated" values are entered by hand from a linked region.

5.8 Extract and verify (D4-03)

Recommended: a "Verification" step kind on target-1 forms. A second reviewer with the verify grant sees the single candidate's answers (exposure recorded; labelled informed), confirms or edits, and the result becomes an attributed gold snapshot with authority = Verified, distinct from Reconciled and from Q-29's accept-as-gold. No IRR for verified forms; exports and the methods summary say "single extraction, verified". Cochrane Handbook ch. 5 accepts one-extracts- one-checks with caveats; without this step teams fake it with target-1 plus informal review and no provenance of the check (SR-12).

6. Risk of bias and reporting quality templates

PROPOSAL, with content ownership and scope put to Chris (D4-06; template ownership D2-15):

Template	Level	Items	Binding
SYRCLE RoB (Hooijmans et al. 2014)	Study, with items 6 (random outcome assessment), 7 (blinding of outcome assessors) and 8 (incomplete outcome data) per outcome	10 items, judgement yes / no / unclear → low / high / unclear risk	Per-outcome items bound to the Outcome Assessment entity (TC1 feature-required type), so judgements are per outcome and cannot be lost
CAMARADES quality checklist (Macleod et al. 2004)	Study	10 items, yes / no	Study level
ARRIVE 2.0 Essential 10 (Percie du Sert et al. 2020)	Study (reporting quality)	10 items with sub-items	Study level

Template rules: items carry semantic roles (rob.domain, rob.judgement, rob.support) so exports produce a domain × study matrix (and domain × outcome where items are per outcome); templates are versioned with a review date and an owner; copies never change when the template does (R1a rule); per-outcome items must be answered per outcome entity. Independence of assessors comes from the ordinary target-2 form plus R4a reconciliation; PRISMA 2020 item 11 (tool, process, number of assessors) is reported by the methods summary. SR-05 cites the little-DOMS investigation as evidence that per-outcome judgements have been lost in ad hoc forms; not re-verified here. Acceptance: AC-R1a-09 and AC-R1a-11 (importing the SYRCLE template yields per-outcome items bound to Outcome Assessment) and an export fixture producing the matrix.

7. Protocol, registration, search documentation and search rounds

7.1 What PRISMA asks for

PRISMA 2020 item 6 (information sources: name, platform, date last searched), item 7 (full search strategies with limits and filters), item 24 (registration details, where the protocol can be found, amendments with reasons); PRISMA-S (Rethlefsen et al. 2021) adds dates of searches, update searches and the deduplication method and counts (item 16). SyRF holds a protocol URL and a search name and file (§2). Amendment F says protocol amendments append, but there is no protocol entity to amend, and Q-26 (profile re-publication) is not tied to an amendment record although a mid-review criteria change is a protocol amendment (SR-04).

7.2 Proposed (D4-05)

• P1, on SystematicSearch (nullable, N-1 rule): searchDate, platform, strategyText or an attached strategy file, limitsAndFilters, dateRange, searchRound and updateOf (SR-24), alongside FEAT-011's sourceType and sourceName; exposed in the upload wizard and the admin source-classification tool (AC-P1-04).
• R3d, or an earlier small release: a project "Protocol and registration" record: registry (PROSPERO, OSF, other; whether PROSPERO accepts the project's animal-review scope is UNVERIFIED), registration ID, URL and date, protocol document link and version, and an append-only amendments log (date, what changed, reason, which profile or form version it corresponds to).
• F5 binding: publishing a profile version whose eligibility rules changed requires an amendment entry ("why it changed" is optional for questions; required for profiles).
• R5b: the PRISMA manifest and the methods summary (§14.1) export all of it.

7.3 Search rounds (minimal now)

searchRound on SystematicSearch and on ExternalStepRecord; report snapshots filterable by round; R5b shows identification per round. Full updated-review support stays deferred; C12 reserves the computation of box 1 from PreviouslyIncluded plus round for later (prisma-flow-diagram-mapping.md:262-268). Box 1 as reported counts is D4-11 (§11.4).

8. Full-text retrieval workflow and amendment M

8.1 The defect

FEAT-011 is internally inconsistent. The taxonomy makes FullTextSought (3) and FullTextNotRetrieved (4) lifecycle states (study-lifecycle-and-source-taxonomy.md:100-102, 148-166), with transitions T4, T12, T13 (:241, :249-250), calls FullTextNotRetrieved terminal (:258), derives box 6 from lifecycle ∧ TA Included (:453) and box 7 from lifecycle (:461), and gives the lifecycle precedence over an Included outcome (:597-601). The mapping document already derives boxes 6, 7, 8, 12, 13 and 14 from Study.fullTextStatus (prisma-flow-diagram-mapping.md:126, 132, 138, 152, 158, 164), and the three-level model defines FullTextStatus {Pending, Sought, Retrieved, NotRetrieved} (three-level-data-model.md: 211-219) while listing both derivations for box 7 (:368). The precedence rule contradicts the plan's "lifecycle = pipeline position" rule and amendment H's per-profile outcomes (SR-15), and nothing in the plan gave a human the action that populates the boxes (SR-02): box 7 would always be 0 and box 8 ≠ box 6.

8.2 Amendment M (new)

Full text: prisma-amendments.md §M.

• Retrieval is fullTextStatus only. Lifecycle never changes for retrieval; T4, T12 and T13 are removed; ordinals 3 and 4 stay reserved and are never written (enum ordinals are appended, never reordered); the precedence rule at :597-601 is deleted; the Included transition (taxonomy rule 6) is unaffected by retrieval.
• Actions (D4-07): Sought (date), Retrieved (how: PDF in SyRF, read externally), Not retrieved (reason from a small controlled list plus free text; author-contact date). Reasons PROPOSAL: not available from any source; paywalled and not obtainable; author contacted, no response; wrong document supplied; language or format not usable; other.
• Actors: project administrators and reviewers with a stage grant (capability placeholder per A-03). Each action is an append-only StudyLifecycleEvent with actor and time (P1 domain model).
• Defaults: a title/abstract collective Include sets Pending → Sought automatically (system actor, recorded). Attaching a PDF (manual link, bulk PDF, study-source upload) only suggests Retrieved; a human confirms. Reading the full text outside SyRF is Retrieved with how = external.
• Admission: full-text steps admit only Retrieved studies (admin override, audited); a Not retrieved study receives no full-text outcome.
• Boxes: 6 and 12 = TA-Included with fullTextStatus ∈ {Sought, Retrieved, NotRetrieved}; 7 and 13 = TA-Included with NotRetrieved; 8 and 14 = Retrieved ∧ entered the full-text pool; each by source column (amendment C). Adopted legacy projects without retrieval history show "retrieval not recorded" coverage, never an inferred Retrieved.
• Releases: P1 (events and actions), R3a/R3b (admission), R5b (boxes). Acceptance: AC-P1-11 and AC-R5b-18 (a study TA-included, marked Not retrieved and never FT-screened appears in boxes 6 and 7 and not in box 8, with the reason exported); FX-PRISMA-05b.

9. Deduplication

9.1 Merge as an alias (amendment L restated)

Brief §1.11, DD-08, V2-02, D2-12. A merge never re-keys immutable records (every natural key carries studyId; C1 forbids editing revisions). The secondary Study gets mergedInto; the primary gets a StudyAlias set. Reads, reconciliation candidate selection, statistics and PRISMA resolve aliases; ContributionQualificationPolicy counts a reviewer once across aliased studies (SF2). When one reviewer reviewed both duplicates, resolution is per reviewer: the current session is chosen (admin choice in the wizard, default the later Complete), the other is superseded with provenance, and the reviewer is counted once. The primary's gold and outcome histories continue; the secondary's gold and outcomes become candidates with lineage, never promoted automatically. Merges and splits run as ADR-020 operations that write both Study documents and refuse busy studies; split removes the alias and re-derives. FEAT-012's "canonical Study" is renamed "primary Study" in amendment L (the plan's "canonical" means the engine).

FEAT-012 scenarios restated by form and profile instead of stage (service-specification.md: 431-437): scenario 2 (one reviewed) is admin-reviewed under amendment D with the reviewed Study as primary (V2-12); scenario 3 (both have evidence on at least one shared form or profile) is an alias merge with candidate joining and per-reviewer resolution; scenario 4 (evidence only on disjoint forms and profiles) is also an alias merge, because sessions belong to forms, not stages, so no "same stage" test exists; PRISMA then counts one study and all its Citations. The FEAT-012 "link only via Publication" outcome is kept for the case where the admin judges the two records to be different studies of one publication (then they are reports, §10).

9.2 QC and reviewer flags

PROPOSAL (SR-19). AutoConfirmed merges are applied before screening; ASySD's specificity above 0.999 (Hair et al. 2023; service-specification.md:54-57) still means some false merges at scale, removing a record from screening silently. P2 adds: an admin QC sample of AutoConfirmed groups shown in the review queue (configurable share; PROPOSAL default 5% with a minimum of 20 groups); a reviewer action "Flag as possible duplicate of…" that creates a DuplicateReviewItem; and manifest fields for the ASySD algorithm version (AlgorithmVersion, :341), tier rules version, the auto-confirmed versus reviewed share, reversals and the QC sample result (PRISMA-S item 16).

9.3 Parity metric (D4-21)

Chris's question states the meaning: pinned R outputs, identical AutoConfirmed groups, ProbableDuplicate pair-set F1 ≥ 0.99, published sensitivity and specificity, 80k citations in under an hour on Bramble. SR-22's concern is folded in as the test design: the pinned fixture includes the normalisation table (case, punctuation, Unicode, DOI prefix) so "identical groups" is testable; every divergent pair is listed for review; sensitivity and specificity on the labelled datasets published with Hair et al. 2023 (names and licences UNVERIFIED; pinned by commit in the fixture) each within 0.5 percentage points of the R package (PROPOSAL); pair agreement is the secondary indicator. AC-P2-01r replaces the retired AC-P2-01 accordingly (AC-21).

9.4 Privacy of Publication and cross-project enrichment (V2-03)

Publication is not "bibliographic data only": FEAT-011 gives it linkedProjectIds[] and per-field provenance with sourceProjectId and sourceCitationId (three-level-data-model.md:97-109), and FEAT-012 enriches it automatically across projects (service-specification.md:415-423, overwriting previous provenance at :422). Rule: reading a Publication never exposes project or citation IDs from projects the caller cannot access; linkedProjectIds and provenance are internal fields served only to platform administrators. A project sees "metadata enriched from another SyRF project (not identified)". Enrichment is a recorded event with an HLC stamp (§1.2), and each as-of export states the Publication metadata version it used; Citations stay the raw, immutable source so an export is reproducible without the Publication. AC-P2 gains a privacy criterion; fixture 8's cross-project part moves to P2 as FX-PRISMA-08a.

9.5 Pool exclusion list (FEAT-012 §12)

Admission (C6) and pool filters exclude lifecycleStatus ∈ {Duplicate, Merged, PendingDuplicateReview, PendingDedupCheck, RemovedByAutomation, RemovedOther} (service-specification.md:646-651); only Active enters pools (taxonomy rule 1, :254). This extends L.5 and AC-P2-06r (V2-12). Withdrawn-search studies and Not retrieved studies at full-text steps are excluded by admission rules, not by lifecycle (amendments J and M).

9.6 External deduplication (K) and box 3

Box 3 = SyRF-detected duplicates (FEAT-012 §11.1) plus reported external duplicates (K); the manifest keeps both parts; FEAT-012 §11.2's count-consistency equation holds over SyRF-held Citations only (V2-13).

10. Reports versus studies and amendments O and N

10.1 Amendment O, report-to-study linkage (D4-08)

Boxes 10 and 16 need "studies" and "reports"; amendment B (open) fixes report identity but nothing groups several papers into one study (SR-07); Cochrane Handbook ch. 4 requires collating reports of the same study, and multiple papers from one experiment are common in preclinical work. Recommended: a "Link reports to one study" action for administrators and reconcilers that creates an append-only StudyLink group (members, reason, provenance, actor; dissolution is an appended event), surfaced in the study view and exports. Linking never merges screening or extraction evidence: each report keeps its sessions, outcomes and gold; extraction stays per report with a group key (later: linked reports' PDFs side by side, follow-up). Counting: a group counts once as a study when at least one member is Included; included members count as reports; an excluded member stays in box 9 with its reason. The duplicate review queue's pair view is reused with a different outcome, "same study, different report" (SR improvement 7). Fixture 9: two reports linked → 1 study, 2 reports in box 10. Until B is approved, exports label totals as records (A-11).

10.2 Amendment N, Citation to Publication link (V2-01)

P1 writes immutable Citations before any Publication exists (P2), yet FEAT-011 makes Citation.publicationId required (three-level-data-model.md:147) and forbids changing a Citation (:167). Recommended: the link lives in an append-only CitationPublicationLink record (citation, publication, how linked: DOI, PMID, fuzzy group, admin; time); Citation.publicationId becomes optional and write-once at creation when the identifier is known; linking never rewrites a Citation (AC-P2 criterion); Study.publicationId stays a mutable pointer. Whether P1 also creates Publications for exact DOI/PMID matches (FEAT-012 Stage 1 brought forward) is an engineering choice at F-P (E92); a link record is needed either way for Stage 2 results.

11. PRISMA accuracy

11.1 Published arithmetic identities (SR-09)

Box-by-box tests are not enough. R5b publishes the identities every snapshot must satisfy, per source column (Database/Register, Other, Unclassified) with explicit remainders that the diagram footnotes and the manifest show (the PRISMA2020 R template assumes equality, which only holds when nothing is pending):

#	Identity	Remainder shown
I1	dbr_total_identified (#31) = database_results (#3) + register_results (#5)	none
I2	other_total_identified (#32) = other_results (#29) = website + organisation + citations + other-source records	none; corrects FEAT-011, whose #32 omits Other records (prisma-flow-diagram-mapping.md:201 versus :211)
I3	total_identified (#33) = #31 + #32	none
I4	records_after_removal (#34) = #33 − duplicates (#7) − excluded_automatic (#8) − excluded_other (#9)	pending dedup review and pending dedup check (FEAT-012 §11.2)
I5	per column: records_after_removal = records_screened + not yet entered screening	"not yet screened" (early stop, batches, unreleased pool)
I6	per column: records_screened = records_excluded + sought_reports + unresolved at title/abstract	pending, conflict, collective Unsure awaiting a vote
I7	per column: sought = not_retrieved + assessed + awaiting retrieval or assessment	Sought and Retrieved not yet in the full-text pool
I8	per column: assessed = excluded_with_reasons + included + unresolved at full text	pending, conflict
I9	Σ reasons = excluded_with_reasons − reason not recorded	reason coverage (amendment E)
I10	new_studies = Σ columns included (resolving StudyLink groups once); new_reports ≥ new_studies	none
I11	total_studies = new_studies + previous_studies; same for reports (D4-11)	none
I12	total_studies_ma ≤ total_studies	none
I13	reported external counts (K) reconcile with the same identities per field, and identified at source − reported removals before import = imported records per search	K's mismatch warning

A mismatch blocks freezing a snapshot unless an administrator records an explanation (as K already does); the explanation is part of the manifest. Acceptance: AC-R5b-09 (field 32 equals field 29: AC-R5b-25); FX-PRISMA-08b (early-stopped, batched review).

11.2 External steps, the entry-phase rule and per-box combination (V2-04)

K lets a project report title/abstract screening, retrieval, assessment and previous-review counts done outside SyRF, but FEAT-011's later boxes depend on SyRF's own outcomes, so a review that screened outside SyRF gets box 6 = 0 and an overstated box 10. Rules (amendment K extension, under Q-37):

• Entry phase per search or import: identified, after deduplication, after title/abstract screening, after retrieval, after full-text assessment (included elsewhere). Records imported after an outside step count as having passed that step: they are not in SyRF's pool-entry or outcome counts for that phase, and the external record supplies the phase's counts with coverage "reported externally".
• Included elsewhere: the import sets lifecycleStatus = Included through admission with the required profiles' outcomes recorded as authority = Imported, coverage "external", so box 10 counts them without inventing SyRF decisions.
• Per-box combination: boxes 2–9 and 11–15 = computed (SyRF) + reported (external) for the same field, both parts in the manifest and the diagram marking "includes n reported outside SyRF"; derived fields #31–#34 are never reported, always computed from their components (K.2 and K.3 agree: identification uses the reported "identified at source" count where one exists, otherwise the imported count, labelled "as imported; processing before import not reported", V2-13); box 1 only from the "previous review version" step type (D4-11); boxes 10, 16 and 17 are computed only.
• No double counting: external screening counts are refused for records that have SyRF decisions at that phase, including imported decisions (§3.6).
• Entry of the other step types (title/abstract screening, retrieval, assessment, previous review) is assigned to R5b's records UI (P1 covers identification and deduplication only).

11.3 Snapshots from authoritative records only (MS-11)

A PRISMA snapshot is computed from Citations, ExternalStepRecords, ScreeningOutcomes, StudyLifecycleEvents, StudyEnteredPool entries (FEAT-011's pool-entry events), StudyLink groups, alias sets and the PrismaPhaseMapping version at the report watermark (an HLC stamp, §1.2), and stored frozen. FEAT-024 rows are never a report input: a source-type dimension there is a catalogue change and retained checkpoints never gain it, and "regenerating a frozen report gives identical numbers" cannot rest on a disposable projection. AC-P1-07 is reworded (acceptance criteria §4.23). Statistics screens may still show FEAT-024 counts; reports do not.

11.4 Box 1 (D4-11)

R5b said "box 1 stays deferred" while K's step types include "studies from a previous review version" (SR-14). Recommended: K populates box 1 as reported counts (previous_studies, previous_reports); when such a record exists the diagram switches to the updated-review template variant and box 16 = new + previous (mapping :264-268); full updated-review support (importing the previous review's included studies with PreviouslyIncluded) stays deferred.

11.5 Withdrawn searches and deletion versus history (D3-12)

Withdrawing a search hides its Studies from pools and from current reports ("excluded from this report: n records from withdrawn search X") but keeps Citations and canonical evidence; its external step records are withdrawn with it; frozen reports never change (amendment J, Q-33). Deleting a whole project follows ADR-014 (24-hour grace, then physical removal with a minimal tombstone, ADR-014-reversible-deletion-and-permanent-tombstones.md:59-74, 142-146, 220-250); PRISMA snapshots do not survive their project, so the user guide tells administrators to export reports before deletion. The canonical collections' place in ADR-014's deletion scope is X-DEL (programme integration), not this page.

11.6 Calibration and Unsure in C12

Calibration records are not pool-entry or screening events. A collective Unsure counts as "not excluded" at title/abstract (box 5 excludes only collective Excluded).

12. Exports for synthesis

12.1 Lane X1, analysis-ready exports (D4-09)

After O1 and R4c: (a) a comparison-level export (gold by default, candidates optional), one row per comparison × timepoint, with the pairing rule derived from Experiment membership and the control flags (a control cohort is one whose treatment units are all flagged control and whose disease-model units match the treatment cohort's; one control serving several treatment cohorts is flagged sharedControl), columns in metafor's escalc() shape (m1i, sd1i, n1i, m2i, sd2i, n2i, dispersion type carried, never converted; direction; units; extractionMethod; experiment, study, report, group key); (b) a machine-readable codebook per export (question identity, version, wording, options, semantic role, entity scope, requiredness; per answer answeredUnderVersion and qualificationPolicy, SR-16) so versioned data (AG3) is interpretable; © a RIS export of any study set (included; excluded with reason; duplicates; not retrieved) from the Citation raw fields. SMD and NMD computation stays outside SyRF; the user guide documents the recipe.

12.2 Extraction export defaults (SR-17)

PROPOSAL (C11, F6a). Under DP6 and EW1 extraction evidence exists for studies that are collectively Excluded or Pending. Extraction exports default to studies whose required profiles (phase mapping) are collectively Included; an explicit option includes others, with per-row collectiveOutcome, surplusAssessment and profileVersion columns. The same default applies to the X1 comparison export. Whether today's annotation export filters by screening outcome is UNVERIFIED (SR-17).

12.3 Synthesis inclusion and metaAnalysisIncluded (SR-20)

AC-R5b-06 names a UI that no release delivers. PROPOSAL: a per-study "Synthesis inclusion" attribute (included, excluded with reason such as no usable data or outcome not reported, not applicable) under a capability placeholder Record synthesis inclusion (A-03), owned by L12 in R5b, exported in R5a and X1 and used by box 17; never derived from extraction completion (C12 rule already).

12.4 Other export columns

goldDiffersFromAllCandidates (SR-18); extractionMethod, nSource (§5); authority and independence on screening exports (§3.6); the near-miss preset (§14.2).

13. Imported decisions, routing, early adoption and related inputs

13.1 FEAT-004 annotation import (D4-14)

FEAT-004 (docs/features/annotation-import/brief.md:22-26, Draft, marked urgent) imports answers from Rayyan, Covidence or spreadsheets through a five-step wizard (:63-82); its open question 2 asks whether imported answers are gold or candidates (:131). Recommended: a lane after R2a; imported answers get provenance kind Imported (source system, import job, mapped reviewer, declaration as in §3.6); they count toward the target only when mapped to a SyRF reviewer and declared independent; they are excluded from default independence statistics; they never become gold automatically; they pin the current question version (:126). The migration writer list's "annotation import" label refers to question-template import (#2781, #3934) and should be corrected by the orchestrator (PH-10).

13.2 Routing studies by answer values (D4-15)

A lane after R4a, not GA: a step-dependency rule on gold values ("only rat studies go to step B"). Methodological rule: routing reads gold or collective outcomes only, never a single candidate's answers, so routing cannot leak one reviewer's decision to another.

13.3 Early screening-profile adoption (D4-16)

FEAT-007's just-in-time adoption (screening-profiles/README.md:172-185) is dropped by the plan (PH-23). Recommended: admin-initiated adoption of screening-only, unreconciled stages after R3b, through a generated manifest, reversible until the first canonical write, with Q-21's compatibility-profile labelling.

13.4 Stale-answer acknowledgement (D4-17)

FEAT-001 D54 and D55 are replaced by RE2's non-blocking warning; enforcement levels are dropped. Consequence: stale answers are surfaced and exported with answeredUnderVersion, never blocked.

13.5 Disabled members' work (D4-20)

Completed work keeps counting and stays in reconciliation because evidence is never erased. An audited admin action can exclude a reviewer's contributions from a form; it is recorded as a withdrawal with reason, never a deletion, and IRR excludes withdrawn contributions.

13.6 FEAT-007 and FEAT-009 as inputs

FEAT-007's success metrics (screening-profiles/README.md:212-217: 80% fewer multi-project workarounds; ≤ 5 minutes to configure a two-stage pipeline; select-next p95 < 400 ms) become R3a/R3b acceptance inputs (PH-23). FEAT-009's reconciliation pool settings (screening-annotations/README.md:348-432: default "reconcile when annotations exist", bypass criteria by question set, all-studies option, and truncation of disagreed sub-reasons) are inputs to the profile reconciliation settings and to amendment E and Q-22: truncation becomes a reason coverage value, "primary agreed; sub-reason not agreed" (PH-24).

14. Transparency outputs

14.1 Methods-summary generator (R5b)

PROPOSAL (SR improvement 1). From data the plan already captures, R5b emits a structured "Methods" block (JSON and prose) covering PRISMA 2020 items 5 (eligibility criteria: profile versions), 6 and 7 (information sources and strategies: §7), 8 (selection process: reviewers, independence, Unsure, conflict route, discussion, calibration, IRR with basis), 9 (data collection: targets, verify or reconcile), 10 (data items: form versions and schemas), 11 (RoB tool and process), 16 (results of selection, with the near-miss list), 24 (registration, protocol and amendments), plus the deduplication method and counts (PRISMA-S item 16), external steps and retrieval failures. It turns the audit trail into publication text.

14.2 Near-miss excluded list

PROPOSAL (SR improvement 2; PRISMA 2020 item 16b). An export preset "full-text excluded studies with primary reason and reviewer or reconciler provenance" in R5a or R5b; the data exists once R3b and R4p ship. Acceptance criterion: AC-R5b-21 (acceptance criteria §4.22).

14.3 Methods caveat label

PROPOSAL (SR improvement 10). Where a project uses single screening, target-1 extraction without verification, or unverified imported decisions, the project overview and the PRISMA manifest carry a persistent "methods caveat" label; the user guide already warns (screening.md:75).

15. Funder alignment

Status: the contract and grant positions are UNVERIFIED beyond docs/funding/ as of 14 March 2026 (D4-18 asks Chris to confirm with the funders). The mapping below is provisional (A-40).

Funder item	Source	Release that satisfies it	Status
NC3Rs Contract 1 Period 4: question editing (annotation questions design interface)	docs/funding/nc3rs.md:172	R1a (templates and shared editor), R2a (versioned forms)	UNVERIFIED whether still expected
NC3Rs Period 4: screening types and study filtering	:173	R3a (steps and routing), R3b (profiles)	UNVERIFIED
NC3Rs Period 4: in-app reconciliation (qualitative)	:174	R4a (form reconciliation and gold); PH Q4's recommendation not to build a reconciler on the legacy model stands	UNVERIFIED
NC3Rs Period 4: customisable project groups (enhanced)	:175	R1c	UNVERIFIED
NC3Rs Period 4: bulk upload of PDFs	:176	FEAT-021 bulk PDF programme (separate; flag off)	UNVERIFIED
NC3Rs "future development": de-duplication; common question templates	:191, :199	P2 (amendment L); R1a	Brought back into scope by this plan
NC3Rs "future development": PDF retrieval automation, machine-assisted extraction, multi-database retrieval, living search, Zotero	:192-198	Out of scope here; living search stays flagged and deferred	Unchanged
SSI RSMF objective 1: annotation question versioning with full audit trails, months 4–8 from a 1 October 2026 start	docs/funding/ssi-rsmf.md:53, 71-73, 44	R2a–R2d	Grant outcome UNVERIFIED (document shows EoI submitted, decision expected April 2026)
SSI RSMF objective 3: WCAG 2.1 AA with an independent audit	:55, :80	GA (D4-18): AC-ALL-07 and AC-GA-08 (WCAG 2.1 AA with an audit step); the accessibility harness in ux-strategy	UNVERIFIED
SSI RSMF objective 5: Community Steering Group and public roadmap	:57, :76	Tester panel (D1-06) and the delivery operating model's public STATUS ledger	UNVERIFIED
SSI RSMF claim: blinding and random serving are core behaviours	:100	D4-19 (§3.8)	Decision pending

16. Decisions needed, engineering items and assumptions

16.1 Decisions (Batch D)

Methodology: D4-01 Unsure; D4-02 discussion route; D4-03 extract and verify; D4-04 calibration; D4-05 protocol, registration and search documentation; D4-06 RoB and reporting-quality templates; D4-07 retrieval actions; D4-08 report linkage (amendment O); D4-09 lane X1; D4-10 graph digitisation; D4-11 box 1; D4-12 IRR basis and methods; D4-13 primary-reason hierarchy; D4-14 FEAT-004; D4-15 routing by answer values; D4-16 early profile adoption; D4-17 D54/D55; D4-18 funder mapping and WCAG audit; D4-19 blinding and random serving; D4-20 disabled members; D4-21 parity meaning. Cross-cutting: D2-12 alias merge; D2-15 template ownership; D3-11 agreement store; D3-12 deletion versus history; D3-25 conversations as audit record. Open questions this page depends on: Q-06b (B, E, F), Q-16, Q-17, Q-22, Q-23, Q-33, Q-37.

16.2 Engineering items E88 to E93

ID	Contract	Lane / contract	Gate
E88	Observation-basis markers and the agreement store: initial-independent-submission marker derived at commit; collective-exposure record at correction (route kinds); "questioned in reconciliation" exposure looked up by session (#3965); imported authority and independence; calibration purpose; computation from canonical revisions into the rebuildable agreement store (D3-11) under the method contract (E9)	L1, L11 / C3, C11	F1a (markers), R5c (store)
E89	Full-text retrieval event model: StudyLifecycleEvent kinds for Sought, Retrieved (how) and Not retrieved (reason list, author-contact date) with actor; automatic Pending → Sought on title/abstract collective Include; the "suggest Retrieved" hook from the PDF programmes; full-text admission on fullTextStatus; box derivations per amendment M	L12, L4 / C12, C6	F-P (P1), F3 (admission)
E90	Extraction provenance and validators: extractionMethod and dataSource roles; unit vocabulary with SI-aware labels and the same-measure validator; dispersion catalogue; domain validators; nSource rule; graph-estimated default on region link; QC view queries	L10 / C14	F-O (O1)
E91	PRISMA arithmetic and authoritative snapshots: the identity checker (I1–I13) with remainders and explanations; entry-phase and per-box combination for external records; computation from authoritative records at an HLC watermark; template-variant switch for box 1; withdrawn-search exclusion	L12 / C12	F6b (R5b); K and L parts at F-P
E92	Link records: CitationPublicationLink (amendment N; whether P1 also creates Publications for exact DOI/PMID matches) and StudyLink groups (amendment O) with alias and group resolution in counting and exports	L12, L1 / C12, C11	F-P (N), P2 (O)
E93	Analysis-ready exports and transparency outputs: comparison pairing rules, codebook schema, RIS tag mapping, Record synthesis inclusion capability and attribute, near-miss preset, methods-summary schema, domain × study RoB matrix	L11, L12 / C11, C10	X1, R5b

16.3 Assumptions

ID	Assumption	Basis	Cost if wrong
A-39	For canonical projects the initial-independent-submission marker can be derived at commit from the commit order and the visibility events already planned (availability messages, VS1 exposure, conversations); for adopted legacy projects it is unknown, and every legacy decision is labelled "basis unknown" in agreement statistics	C3 three-state exposure; EX2 no fabricated history	R5c shows no IRR for adopted projects, only percent agreement labelled "basis unknown"; or an explicit marker must be written by every submit path
A-40	The funder mapping in §15 reflects docs/funding/ as of 14 March 2026; neither the NC3Rs contract position nor the SSI RSMF outcome has been confirmed since	docs/funding/nc3rs.md, docs/funding/ssi-rsmf.md	Release order could change (for example R4a earlier for NC3Rs); WCAG audit timing could move

16.4 Follow-up backlog (not in this scope)

A graph digitiser lane (after O1 pilots, D4-10); full updated-review support with PreviouslyIncluded; linked reports' PDFs side by side in extraction; registry lookups (PROSPERO, OSF); direct connectors to Covidence or Rayyan (FEAT-004 brief rules them out); scored training against gold as an admission prerequisite (hook reserved by D4-04); statistical outlier checks on extracted values.

Resolution record

Finding	Category	Where	Note
SR-01	Adopted	§4.1–§4.3, §16.2 E88; contracts C3, plan R5c, AC-R5c-06, 10, 11 and 12	IRR observation basis in C3 (PROPOSAL); screening IRR per profile in R5c; methods under D4-12
SR-02	Adopted	§8; prisma-amendments M, plan P1 row, AC-P1-11, AC-R5b-18	Human retrieval workflow; actors and PDF suggestion are D4-07
SR-03	Adopted	§3.6; contracts C3, prisma-amendments H authority list	authority = Imported, independence declaration; K no-double-count
SR-04	Question	§7; D4-05	Search fields in P1 and the protocol record adopted as PROPOSAL pending D4-05
SR-05	Question	§6; D4-06, D2-15	Template rules and AC-R1a-09 and AC-R1a-11 proposed
SR-06	Adopted	§5.1–§5.5; contracts C14, plan O1 row, AC-O1-02, AC-O1-11 and AC-O1-12	Graph digitiser decision is D4-10
SR-07	Question	§10.1; prisma-amendments O	D4-08; FX-PRISMA-09
SR-08	Question	§12.1; plan lane X1 row, AC-X1	D4-09
SR-09	Adopted	§11.1; contracts C12, AC-R5b-09 and AC-R5b-25	Also Corrected: FEAT-011 #32 omits Other records (I2)
SR-10	Question	§3.5; AC-R3b-13 (failing-criteria view: AC-R4p-09)	D4-13
SR-11	Question	§3.4	D4-04; C12 rule and C6 hook
SR-12	Question	§5.8	D4-03
SR-13	Question	§3.2	D4-01
SR-14	Corrected	§11.4; plan R5b scope, prisma-amendments K, AC-R5b-07	R5b and K were inconsistent; box 1 from K per D4-11
SR-15	Corrected	§8.1–§8.2; prisma-amendments M and summary table	Lifecycle precedence superseded; recorded for register §2
SR-16	Adopted	§12.1 (codebook columns)	Compatibility guards themselves are decided in versioning-model.md (brief §1.9)
SR-17	Adopted	§12.2; AC-R5a-10	Default by collective outcome; surplus labelling
SR-18	Adopted	§4.5, §12.4	Override count and export column
SR-19	Adopted	§9.2; prisma-amendments L, AC-P2-17	QC sample, reviewer flag, manifest fields
SR-20	Adopted	§12.3; plan R5b scope	Owner L12, R5b; capability placeholder
SR-21	Adopted	§3.1	PROPOSAL template defaults; depends on D4-01, D4-02, D4-13
SR-22	Question	§9.3; AC-P2-01r	D4-21 as Chris stated, with divergent-pair listing and the 0.5 pp tolerance as test design
SR-23	Question	§3.3	D4-02
SR-24	Adopted	§7.3; plan P1 row	Minimal search rounds now
SR-25	Adopted	§3.7	Per-profile option, default off
SR improvement 1	Adopted	§14.1; plan R5b scope	Methods-summary generator
SR improvement 2	Adopted	§14.2; AC-R5b-21	Near-miss list
SR improvement 3	Adopted	§4.6	Drift view
SR improvement 4	Adopted	§3.5	Failing-criteria vectors in R4p
SR improvement 5	Adopted	§5.6	Extraction QC view
SR improvement 6	Adopted	§9.2; prisma-amendments L	Dedup transparency in the manifest
SR improvement 7	Adopted	§10.1	Conditional on D4-08; side-by-side PDFs are follow-up
SR improvement 8	Adopted	§12.1	Codebook in X1
SR improvement 9	Adopted	§3.1, §6	Content ownership by CAMARADES methodologists (D2-15)
SR improvement 10	Adopted	§14.3	Methods caveat label
SR Q-1	Question	§3.2	D4-01
SR Q-2	Question	§3.3	D4-02
SR Q-3	Question	§5.8	D4-03
SR Q-4	Question	§3.4	D4-04
SR Q-5	Question	§7	D4-05
SR Q-6	Question	§6	D4-06
SR Q-7	Question	§8.2	D4-07
SR Q-8	Question	§10.1	D4-08
SR Q-9	Question	§12.1	D4-09
SR Q-10	Question	§5.7	D4-10
SR Q-11	Question	§11.4	D4-11
SR Q-12	Question	§4.3	D4-12
SR Q-13	Question	§3.5	D4-13
V2-01	Adopted	§10.2; prisma-amendments N, AC-P1-12	Link record; Citation never rewritten
V2-02	Corrected	§9.1; prisma-amendments L	Alias merge; scenarios by form and profile; E33 restated
V2-03	Corrected	§9.4; prisma-amendments L rule 7, AC-P2-15, FX-PRISMA-08a	Privacy rule; enrichment events; as-of basis
V2-04	Corrected	§11.2; prisma-amendments K, AC-R5b-07	Entry-phase rule; per-box rules; box 1 via D4-11; under Q-37
V2-10	Corrected	prisma-amendments G	Lines 279–280; MIG-13 and MIG-14 covered
V2-11	Corrected	prisma-amendments H	All three placeholders amended; Imported added
V2-12	Corrected	§9.1, §9.5; prisma-amendments L, AC-P2-04, AC-P2-06r, AC-P2-01r	Scenario 2 change listed; exclusion list extended; criteria fixed
V2-13	Corrected	§9.6, §11.2; prisma-amendments K	K.2 and K.3 agree; #31–#34 never reported; FEAT-012 §11 in Amends; §11.2 over SyRF-held Citations; other step types assigned; withdrawn searches
V2-14	Corrected	prisma-amendments preamble	Freeze timing and Q-37 cited
PH-10	Question	§13.1	D4-14; inventory label correction for the orchestrator
PH-12	Question	§15, §3.8	D4-18 and D4-19; traceability table provided; AC-ALL-07 and AC-GA-08 wording in acceptance criteria
PH-23	Question	§13.3, §13.6	D4-16; metrics as acceptance inputs
PH-24	Adopted	§13.6	FEAT-009 settings and truncation as inputs to E and Q-22
PH question 4	Question	§15	D4-18
PH question 5	Question	§3.8	D4-19
PH question 6	Question	§13.1	D4-14
PH question 9	Question	§13.3	D4-16
review AC-04	Adopted	acceptance criteria §7 fixtures FX-PRISMA-01..09	Versioned data with per-release evidence assertions; splits by release
review AC-20	Adopted	AC-P1-09.., AC-P2-10.., AC-R3a-18 and 19, AC-R5b-08.., AC-C1-06	FEAT-011 MUSTs as criteria; validation procedures reused
review AC-21	Adopted	§9.3; AC-P2-01r, AC-P2-06r and AC-P2-11 to 14	Metric per D4-21; datasets and licences UNVERIFIED
MS-11	Corrected	§11.3; contracts C12, AC-P1-07	Authoritative-only snapshots; AC-P1-07 reworded
DD-08	Corrected	§9.1; prisma-amendments L	Alias merge; "primary Study"
NS-06	Adopted	§4.1; contracts C3, AC-R5c-07	"Questioned in reconciliation" exposure kind; R5c, C11 and R6 consume it; D3-25