[P0] Reclassify Zotero literature for CWL ontology libraries

[seonghobae]

Live baseline

• Zotero Local API http://127.0.0.1:23119/api/ remains read-only for the recorded Zotero 9.0.6 / API v3 local campaign; last recorded immutable read-only snapshot is library version 12341, 8,326 observed records.
• Query/classifier output is discovery/proposal evidence, never authoritative classification.
• Zotero 10+ reviewed write paths remain separately gated by user authorization, exact server/item/library preconditions, reversible receipts and the provider transport boundary.
• Provider-defined Local API write transport is loopback HTTP. Zotero-Server-ID is database-instance continuity/precondition evidence, not cryptographic peer authentication; same-host API-key confidentiality remains a release boundary unless protected transport appears or governance explicitly narrows the supported threat model.

Current successor authority — 2026-09-05

The full Draft chain was non-force restacked after the Foundation product/technical gap baseline refresh. Every successor retains its previous semantic head as first parent and adopts the current direct parent as second parent; no force-push/destructive rebase or predecessor-evidence transfer occurred.

#9 256076d -> #10 b821b0f -> #11 cb365fb -> #12 5ce1a18 -> #13 821b04c -> #15 64cb10f -> #16 d02d0f9 -> #17 47e86b5 -> #18 bb8ef8c -> #19 b6c11b2 -> #20 53a91d3 -> #21 d51762d -> #22 2c8ee56 -> #23 17a0407 -> #24 005826d -> #25 8a239ee -> #26 0f5002e -> #27 9d89805 -> #28 2de9254 -> #29 98204ff -> #30 ddd0e4c -> #31 e5a1e52 -> #32 0ac89b6 -> #33 4feb387 -> #34 062a0d9

Foundation is #1 b538470c963e6524ddc0c3f652a46a4fc8265150. All Zotero successors remain Draft and require their own unchanged exact-head protected evidence after the restack.

Preserved contracts and unresolved release boundary

#15 retains receipt binding to review/authority/server/Zotero-version/library/rule/snapshot coordinates, complete DryRun not-attempted enumeration, and conditional inverse evidence only when server/item identity remains proven. #18 keeps the loopback-HTTP provider threat explicit and does not authorize an enterprise-secure live-write claim. #30's private-input boundary rebuilds metadata/open paths from an authorized canonical parent plus filename and keeps O_NOFOLLOW, exact 0600, single-link and bounded-input checks. #33 provides deterministic non-reserving steward batches. #34 reconstructs and compares the exact human-visible batch context before converting decisions to the atomic patch, and its production output validator rebuilds the output path from the authorized canonical parent plus final filename before create-new writing.

These are source contracts, not inherited hosted GREEN. The complete steward-review denominator remains 3,715 proposals; unverified worksheet decisions remain 0/3,715, and externally approved steward labels independently remain 0/3,715. No live steward decision, Zotero write/rollback, governed publication or immutable release is claimed.

Acceptance boundary

Acceptance still requires one immutable top-level bibliographic snapshot, one proposal per paper, complete item/library/rule/snapshot provenance, reversible duplicate review, default dry-run, Zotero 10+ reviewed-authority/precondition/transport gates, reversible write evidence, 100% owned production coverage, complete steward review rather than sampling, exact-head required workflows and review, and code-current PRD/TRD/ADR/security/threat-model/gap documentation. Descendant evidence never back-proves an unresolved predecessor.

Issue #8 remains open.

[seonghobae]

2026-09-04 successor/progress correction

PR #9 now carries the first executable read-only Zotero classification slice at exact head 5cda60e2b218034dd5abde9bc527bcc271e92eb9, stacked on Foundation a379c7230253c3aaa0c6fc8486cc39be421eca35. The branch incorporates the valid CodeRabbit/Codex findings: deterministic abstention reasons, replayable matched metadata, legacy dx.doi.org normalization, conflicting-family abstention, injectable/tested snapshot-reader core, Local API v3/schema-42 pinning and drift checks, whole-snapshot item/byte budgets, temp-only create-new output with explicit flush, Zotero ACL entry in the Context Map, and source-coordinate coverage accounting. All currently returned inline review threads are resolved after current-head verification.

The PR is intentionally Draft again because Foundation is still non-terminal. Product run 33877322525, job 101037300401, is exact-head queued before runner assignment (ubuntu-24.04, runner_id=0, steps=[]), so local verification is not hosted GREEN.

Issue #8 remains open. No Zotero mutation/write-back has been implemented. The next repository-owned RED after Foundation terminal evidence is a steward-reviewed golden set for disposition precision/recall and multilingual coverage without weakening abstention safety. Zotero 10+ write-back still requires authenticated server identity, fresh object/library-version preconditions, item-by-item before/after receipts and rollback evidence.

[seonghobae]

2026-09-04 research-stack correction: #9/#10/#11 have all been returned to Draft because Foundation is not integrated. #10 current head is d5ccd73ae3b23154305d2ec51d24a00c71f23f6d; #11 current head is c28fccaa592d6cbb0dcf9d86d0558bdb28d43842. Fresh #11 review triage rejected one invalid P1 request to mix derived audit_summary into the raw Zotero source-snapshot digest; TRD §11 and the public API define that digest as canonical raw-item content identity, so the thread was resolved with contract rationale. A second P2 finding was valid: provenance-complete proposals could retain a linked child with a blank Zotero key. Test-only b836db... encoded the parent+blank-child regression but was cancelled before execution when concurrent successor c28fcc... added the minimal predicate requiring nonblank parent and every retained child key. That repair is adopted without claiming executed RED->GREEN; #11 Product 33883722090 is queued and the P2 thread remains unresolved until exact-head verification. No Zotero mutation or authority promotion was introduced.

[seonghobae]

2026-09-05 successor evidence update

The active stack now preserves and extends every Zotero reclassification delta without closing predecessors:

• PR feat(research): add reversible duplicate review manifest #12 exact head e77a2d232ca77a7bf8d474141d33f48da451415b repairs transitive duplicate components, binds the reviewed set to complete item-key/item-version coordinates, and includes every component source revision in each reversible canonical operation.
• PR feat(research): add reviewed Zotero dry-run write plan #13 exact head f31dd75da94a65f16949a78cccfa009fa430c0a7 non-force restacks feat(research): add reversible duplicate review manifest #12 and retains the default-dry-run reviewed collection/typed-tag plan.
• PR feat(zotero): emit reversible write execution receipts #15 exact head 9f1913cbd3236259d0f450b7373c6986970a0252 adds complete preflight, item-wise post-state verification, secret-free partial-failure evidence, and reverse-ordered rollback operations. It contains no API key or HTTP mutation adapter.
• PR test(zotero): verify multilingual abstention safety #16 exact head 28ca5311375f9c3d094a2c4b1f7b2ecd650d9a8f proves Korean, Japanese, Chinese, Vietnamese, Spanish, German, and French ontology-alignment metadata abstains fail-closed, while the English evidence-backed rule remains the positive control. This is safety coverage, not translated classification support.

Local verification on the #16 head passed workspace fmt, clippy, tests, and the repository coverage gate with owned Rust source coordinates at 1381/1381 regions and 250/250 branches. Protected-main integration is not claimed: Foundation remains review-required with queued required jobs, and stacked successors are not independently mergeable before their parents. AC4 still needs real steward decisions for all 49 live duplicate groups. AC6 still needs an authenticated Zotero 10+ adapter and approved live write/partial-failure/rollback evidence; the installed runtime remains Zotero 9.0.6.

[seonghobae]

2026-09-05 exact-head correction

The active Zotero stack remains open and delta-preserving. PR #13 is now bd855ef7c85c67f8026480743b7540c50dcf55c3; its reviewed write plan binds Zotero version plus the complete item-key/item-version snapshot, rejects detached revisions and unsupported tag types, and canonicalizes manual tag markers. PR #15 is now 2dfdf0c8f49601ab95958a216258099874dbbd22; it reconciles failed or invalid write responses through the same read boundary, includes proven committed-but-response-lost items in rollback evidence, marks unprovable state indeterminate, and seals all execution-critical plan fields against post-validation forgery. PR #16 is now 6dada71a17446a77be8c55e23a1cc67ef2d145b8; every Korean, Japanese, Chinese, Vietnamese, Spanish, German, and French fixture must produce the explicit unsupported-vocabulary abstention, with English retained as the positive control.

On the current #16 head, workspace tests, clippy with warnings denied, CI contract validation, and the repository coverage gate pass; owned Rust source coordinates are 1484/1484 regions and 264/264 branches. Independent exact-object reviews report no remaining finding for current #13 and #15. Hosted Codex review is currently quota-limited and does not supply current-head approval. No protected merge is claimed: Foundation #1 remains REVIEW_REQUIRED with required jobs queued, so the stack cannot yet integrate. AC4 still needs steward decisions for all 49 live duplicate groups; AC6 still needs an authenticated Zotero 10+ transport and approved live write/rollback evidence.

[seonghobae]

2026-09-05 successor update

Draft PR #17 (01c7fa5bc7edac2f2b6ad47030062ffab7ebb956) now carries the missing owner-owned Zotero 10+ authenticated Local API transport on top of PR #16. Independent exact-object review first found that single-item Last-Modified-Version had been misread as a library version and that PATCH could not atomically enforce both library and item freshness. The repaired transport performs a stable library-version/read/item-version/read/library-version sequence and uses one-item POST /api/users/0/items with library If-Unmodified-Since-Version plus the item key/version in the body. It validates the server partition, exact returned key, advanced versions, complete collections/tags, bounded response, and keeps the API key private and absent from errors/serialization.

Fresh local evidence on #17: workspace tests, strict clippy, CI contract validation, and coverage pass; owned Rust source coordinates are 1736/1736 regions and 294/294 branches. Final independent re-review found no remaining issue. This is transport contract evidence only: the installed Zotero remains 9.0.6, so approved live Zotero 10 write, partial-failure, and rollback proof remains incomplete. #17 is Draft behind the unintegrated stack; no protected-main merge is claimed.

[seonghobae]

PR #18 now carries the Zotero 10 Local API authorization lifecycle at exact head 6e333aea4bdfa8b0b2d40a623ed7c69bb7bfb4a8, stacked on PR #17 exact head 01c7fa5bc7edac2f2b6ad47030062ffab7ebb956.

Independent review found and the branch repaired two root defects before publication: a write 412 now verifies the response server before classifying library staleness, and authorization 403 is treated as user denial only when the exact server matches and bounded JSON proves {"denied":true}. Full Rust 1.98 workspace tests, strict Clippy, CI contract, and owned coverage (1,866/1,866 regions; 310/310 branches) pass.

Still not claimed: a live Zotero 10 approval prompt, remembered key behavior, approved write, partial-failure recovery, or rollback execution. PR #18 remains Draft while the parent and protected gates remain unresolved.

[seonghobae]

PR #18 advanced to exact head ec116a45102d774db236684a48bdd704188ec338. CodeRabbit identified that read-path 412 responses could hide a Zotero database switch; the library preflight and item GET now bind response server identity before generic status handling, with both stages covered by regression fixtures. Full Rust 1.98 validation and owned 100% region/branch coverage pass. Live approval, write, partial-failure, and rollback evidence remain open.