Seeded repo

workplans/INDEX.md

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+# Execution plan and dependency map
+
+| ID | Workplan | Prerequisites | Milestone |
+|---|---|---|---|
+| WP-00 | Upstream baseline & IP audit | none | Reproducible reference and extraction decision |
+| WP-01 | Canonical contracts & fixtures | none; coordinate with WP-00 | Two independent dataspaces pass contract |
+| WP-02 | UI extraction & experience skeleton | WP-00 + WP-01 | First generic explorer end-to-end |
+| WP-03 | Ingestion & publishing | WP-01 (parallel WP-02) | Repeatable snapshots with evidence |
+| WP-04 | Relations & journeys | WP-02 + WP-03 | Graph navigation |
+| WP-05 | Quality & parity | begins WP-00, closes WP-04 | Release candidate |
+| WP-06 | External pilot | WP-05 | Decision to expand |
+
+**Minimum viable proof:** WP-00 → WP-01 → WP-02, with JSON snapshot ingestion; WP-03 provenance gate is required before any externally ingested public content is published. WP-04+ need not delay the basic demo.
+
+Each workplan has a deliverable, tasks, verification gates and risks. No effort estimates are asserted before cloning and profiling the upstream code. Proposed priority: WP-00/01 now; WP-02 then WP-03; WP-04/05; pilot WP-06.
+
+- **WP-07** — Opt-in, authorized OnCo reference-slice conformance and paired upstream behavioral tests (see `WP-07.md`).

workplans/WP-00.md

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+# WP-00 — Upstream baseline & IP audit
+
+**Purpose:** Reproduce OnCo baseline and establish legal, behavioral and visual reference.
+
+**Dependencies:** see `INDEX.md`. **Status:** planned. **Owner:** to assign. **Estimate:** to refine after WP-00.
+
+## Work packages
+
+- [ ] Pin immutable upstream git SHA and preserve original MIT license/NOTICE.
+- [ ] Install exactly locked dependencies; run build/test/lint/typecheck and record results.
+- [ ] Trace dependencies of browser, detail, graph, navigation and data.
+- [ ] Capture responsive screenshots and keyboard interaction walkthrough.
+- [ ] Inventory data, code, logos, artwork, fonts, external dependency licenses.
+- [ ] Quantify oncology-specific references and decide component-by-component reuse.
+
+## Acceptance gates
+
+- [ ] Pinned SHA, baseline report and component inventory committed.
+- [ ] License matrix separates MIT software from NC dataset/assets.
+- [ ] One reference example each for browse/detail/search/relations captured.
+
+## Key risk / mitigation focus
+
+R1: license/source boundary; R2: unable to reproduce baseline. Log evidence and deviations in the workplan review before marking complete.
+
+## Evidence artifacts
+
+Pull requests, test logs, pinned artifacts, screenshots or comparison report where applicable. Add explicit `ImplementationNotes.md` and `Review.md` on completion; do not mark a gate passed without a verifiable link.

workplans/WP-01.md

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+# WP-01 — Canonical contracts & 2-domain fixtures
+
+**Purpose:** Establish source-independent knowledge projection and the zero-UI-code-change experiment.
+
+**Dependencies:** see `INDEX.md`. **Status:** planned. **Owner:** to assign. **Estimate:** to refine after WP-00.
+
+## Work packages
+
+- [ ] Freeze v0.1 snapshot schema and manifest schema; document migrations.
+- [ ] Model entity IDs, kinds, directed relations, evidence and claims in TS/Zod.
+- [ ] Normalize systems-thinking and software-architecture fixtures with independently authored prose.
+- [ ] Write duplicate, dangling, cyclic non-taxonomy and missing-source tests.
+- [ ] Define policy for unknown and conflicting facts.
+
+## Acceptance gates
+
+- [ ] Both fixtures validate and supply ≥3 kinds and ≥8 entities each.
+- [ ] A shared renderer can switch manifests with no domain vocabulary in UI source.
+- [ ] Snapshot format documented and versioned.
+
+## Key risk / mitigation focus
+
+R3: abstractions erase domain semantics. Log evidence and deviations in the workplan review before marking complete.
+
+## Evidence artifacts
+
+Pull requests, test logs, pinned artifacts, screenshots or comparison report where applicable. Add explicit `ImplementationNotes.md` and `Review.md` on completion; do not mark a gate passed without a verifiable link.

workplans/WP-02.md

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+# WP-02 — UI extraction & experience skeleton
+
+**Purpose:** Deliver the strongest OnCo-style interaction patterns on generic data.
+
+**Dependencies:** see `INDEX.md`. **Status:** planned. **Owner:** to assign. **Estimate:** to refine after WP-00.
+
+## Work packages
+
+- [ ] Extract/port UI tokens, layout, header, hero and reusable table from pinned upstream.
+- [ ] Create registry-based kind index and entity detail with no oncology imports.
+- [ ] Adapt BrowserRow via a pure mapper and add configurable generic cell renderers.
+- [ ] Preserve shareable URL query, facets and sorting; test browser back/forward.
+- [ ] Implement keyboard search, empty/loading/error states and responsive layouts.
+
+## Acceptance gates
+
+- [ ] Browse/search/filter/sort/detail works for two dataspaces.
+- [ ] Component dependency check prohibits `/oncology|cancer|drug|target/` domain imports in generic code.
+- [ ] Copying upstream components retains provenance headers/notices.
+- [ ] Keyboard and small-screen smoke tests pass.
+
+## Key risk / mitigation focus
+
+R4: extraction too expensive; use greenfield component where warranted. Log evidence and deviations in the workplan review before marking complete.
+
+## Evidence artifacts
+
+Pull requests, test logs, pinned artifacts, screenshots or comparison report where applicable. Add explicit `ImplementationNotes.md` and `Review.md` on completion; do not mark a gate passed without a verifiable link.

workplans/WP-03.md

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+# WP-03 — Ingestion, provenance & publishing
+
+**Purpose:** Turn raw inputs into trustworthy reproducible snapshots.
+
+**Dependencies:** see `INDEX.md`. **Status:** planned. **Owner:** to assign. **Estimate:** to refine after WP-00.
+
+## Work packages
+
+- [ ] Implement build-time JSON/NDJSON and Markdown frontmatter connector APIs.
+- [ ] Make import idempotent with source digests and connector version.
+- [ ] Resolve links in second pass; report dangling/conflicts; distinguish tombstones.
+- [ ] Model source licenses, citations and attribution; quarantine unsupported content.
+- [ ] Generate snapshot, manifest and machine/human import reports; atomic publication.
+
+## Acceptance gates
+
+- [ ] Two connector types produce identical normalized snapshots for equivalent input.
+- [ ] Repeated ingest yields same content hash.
+- [ ] Every published sourced claim has a retrievable evidence reference.
+- [ ] Rights violations prevent publication.
+
+## Key risk / mitigation focus
+
+R5: rights metadata missing; quarantine instead of guessing. Log evidence and deviations in the workplan review before marking complete.
+
+## Evidence artifacts
+
+Pull requests, test logs, pinned artifacts, screenshots or comparison report where applicable. Add explicit `ImplementationNotes.md` and `Review.md` on completion; do not mark a gate passed without a verifiable link.

workplans/WP-04.md

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+# WP-04 — Relation explorer & knowledge journeys
+
+**Purpose:** Make interconnected knowledge truly explorable.
+
+**Dependencies:** see `INDEX.md`. **Status:** planned. **Owner:** to assign. **Estimate:** to refine after WP-00.
+
+## Work packages
+
+- [ ] Implement typed outgoing/incoming relation blocks and inverse labels.
+- [ ] Build bounded interactive 1-2 hop graph and adjacency export.
+- [ ] Add collections, related objects, reading path breadcrumbs.
+- [ ] Introduce optional glossary tooltips and link previews.
+- [ ] Handle cycles, multigraph, multi-parent hierarchy and disconnected components.
+
+## Acceptance gates
+
+- [ ] No graph relation omitted silently.
+- [ ] Graph focus and detail navigation are reversible and deep linkable.
+- [ ] Large graph safeguards tested with synthetic fixture.
+
+## Key risk / mitigation focus
+
+R6: large graph performance. Log evidence and deviations in the workplan review before marking complete.
+
+## Evidence artifacts
+
+Pull requests, test logs, pinned artifacts, screenshots or comparison report where applicable. Add explicit `ImplementationNotes.md` and `Review.md` on completion; do not mark a gate passed without a verifiable link.

workplans/WP-05.md

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+# WP-05 — Quality system & upstream experience parity
+
+**Purpose:** Measure architectural independence and UX faithfulness.
+
+**Dependencies:** see `INDEX.md`. **Status:** planned. **Owner:** to assign. **Estimate:** to refine after WP-00.
+
+## Work packages
+
+- [ ] Automate schema/ingest/ui/e2e tests and two-domain switch tests.
+- [ ] Run accessibility, screenshot comparison, core web vitals and responsive audits.
+- [ ] Report provenance completeness, stale counts, unresolved refs and ingestion failure classes.
+- [ ] Document deviations from upstream and verify third-party notices.
+- [ ] Harden inputs and public snapshot generation.
+
+## Acceptance gates
+
+- [ ] Tests run in CI; no material keyboard accessibility failures.
+- [ ] Two unrelated domains pass all critical journeys.
+- [ ] Source and license completeness report available.
+
+## Key risk / mitigation focus
+
+R7: tests approximate but do not prove usability. Log evidence and deviations in the workplan review before marking complete.
+
+## Evidence artifacts
+
+Pull requests, test logs, pinned artifacts, screenshots or comparison report where applicable. Add explicit `ImplementationNotes.md` and `Review.md` on completion; do not mark a gate passed without a verifiable link.
+
+## Reference-oracle testing extension
+
+Add WP-07: compare the *same permitted pinned OnCo slice* through the original implementation and generic Content Explorer, including behavioral journeys and visual snapshots. Public CI remains synthetic-only.

workplans/WP-06.md

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+# WP-06 — Extensibility & first real-world pilot
+
+**Purpose:** Attach an independently maintained knowledge source and validate user value.
+
+**Dependencies:** see `INDEX.md`. **Status:** planned. **Owner:** to assign. **Estimate:** to refine after WP-00.
+
+## Work packages
+
+- [ ] Implement third connector (GitHub issues or Wikidata after rights/rate review).
+- [ ] Provide connector authoring template with fixture-based certification tests.
+- [ ] Pilot one non-medical viable infospace with real users.
+- [ ] Prioritize API/JSON-LD/MCP/ASK enhancements from observed needs.
+- [ ] Define long-term update and governance responsibilities.
+
+## Acceptance gates
+
+- [ ] Third connector is refreshable and auditable.
+- [ ] Pilot uses no hardcoded kinds in UI.
+- [ ] Document informed go/no-go for dynamic deployment and search backend.
+
+## Key risk / mitigation focus
+
+R8: third-party API policies and data quality. Log evidence and deviations in the workplan review before marking complete.
+
+## Evidence artifacts
+
+Pull requests, test logs, pinned artifacts, screenshots or comparison report where applicable. Add explicit `ImplementationNotes.md` and `Review.md` on completion; do not mark a gate passed without a verifiable link.

workplans/WP-07.md

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+# WP-07 — OnCo licensed reference-slice conformance
+
+**Purpose:** validate generic Content Explorer against real OnCo topology and the OnCo UX using a small pinned, authorized cancer-data slice, without copying the broader corpus.
+
+**Dependencies:** WP-00 license/behavior audit; WP-01 model; WP-02 UI; WP-03 connector; WP-05 test harness. **Status:** planned and BLOCKED on data-use authorization.
+
+## Tasks
+- [ ] Determine test operator/use, acquire permission/license where required by OnCo `LICENSE-DATA`; document decision and redistribution restrictions.
+- [ ] Pin upstream SHA and capture behavior for ~12–25 representative entities, 8+ user journeys, and several viewport sizes.
+- [ ] Build allowlist-only `onco-reference` adapter from explicitly authorized local inputs to canonical snapshot, retaining provenance, dates, rights and record links.
+- [ ] Implement graph topology, inverse-links, search/facet, detail, source display, stable deep-link and negative mutation tests.
+- [ ] Run paired OnCo/Content Explorer Playwright tests against pinned source baseline; report semantic and visual divergences separately.
+- [ ] Run clean-room public CI with synthetic domains and no actual OnCo dataset; audit that no OnCo corpus entered distributable packages/build artifacts.
+
+## Gate
+No real data import until authorization; no missing attribution or silent relation loss; version-pinned reproducibility; comparative conformance report and documented exceptions. For full process see `tests/onco-reference/README.md`.