feat(openontology): Phase 2 + Phase 3 — storage, REST/SSE, MCP, RDF/SHACL, adapters, TUI, explorer (#101)

Everything the two shipped PRD phases deferred, minus what is called out below.

Storage (Phase 2)
  @logicsrc/openontology gains a SQLite/Turso adapter. It hydrates the read
  model at open, serves reads synchronously — a query evaluator that awaits per
  triple pattern is unusable — and buffers mutations as SQL that flush() writes
  in one transaction. Versioned idempotent migrations; indexes over subject,
  predicate, entity-valued object, status, both time axes, aliases, and external
  ids; FTS5 for label/alias search. The append-only status log is replayed on
  open, so retractions, supersessions, and merge redirects survive a reopen.

REST + SSE + OpenAPI (Phase 2)
  16 paths under /api/ontologies in logicsrc-web, described at
  /api/ontologies/openapi and referencing the published JSON Schemas rather
  than restating them. No token is read-only; a curator token can apply; an
  agent token can propose and cannot apply. Idempotency-Key on mutations,
  revision ETags, 409 on a stale base revision, and an SSE stream that emits
  the same event objects as the JSON endpoint.

MCP (Phase 2)
  OpenOntology and OpenPRD surfaces on the standards server: spec/manifest/
  schema/queries and PRD spec/index as resources, 11 ontology tools and 6 PRD
  tools, 7 prompts. Read-only by default; OPENONTOLOGY_MCP_WRITABLE=1 buys
  proposals, never applies — the denial is the shared policy layer, not a
  second rule that could drift.

Interoperability (Phase 3)
  RDF/Turtle export and import of the reified profile, plus the plain triple
  for asserted relationships so a consumer wanting only the accepted graph gets
  one. SHACL for 5 of 7 constraint kinds; `unique` and `query` are reported as
  unmapped in both the return value and the generated Turtle, because a shape
  that quietly means something narrower is worse than no shape.

Source adapters (Phase 3)
  CSV, JSON, YAML, NDJSON, Markdown, generic JSON HTTP, and GitHub. All produce
  PROPOSED change-set operations with source, evidence selector, run id, and
  confidence attached; fetch is injected so ingestion is offline and testable.
  Each declares its capabilities, so "nothing was deleted upstream" is never
  confused with "this adapter cannot see deletions" — none of the seven can.

TUI + explorer
  Keyboard-first panels (types, entities, claims, sources, queries, change
  sets, validation, audit) as plain strings that survive SSH and 60 columns;
  status is a glyph and a word, never colour alone; the key bar wraps rather
  than truncating. Wired as `logicsrc ontology tui`. A read-only web explorer
  at /openontology/explore with entity and claim views showing status, both
  clocks, confidence, sources, evidence, and append-only history — plus an
  /openprd page for the companion standard.

Bugs found and fixed while testing
  - the API built a new engine per request, so `explain` could never find a
    resultId from a prior request; engines are now cached per role
  - the TUI status bar called engine.validateOntologyPackage(), appending a
    package.validated event on every repaint; it now uses the pure validator

Verification: 76 new tests (527 total across the monorepo, all passing); full
build green; the libSQL adapter is exercised against real files, the API
through its route handlers, and MCP over an in-memory transport.

Not included: PWA review/approval write flows (they need an auth story this
deployment does not have), OWL/RDFS mappings, SPARQL/Cypher/Datalog query
adapters, and Phase 4 governed actions. The compatibility matrix marks those
"planned", not "supported".

Refs: prd/0001-add-logicsrc-openontology-spec.md

Co-authored-by: Claude Opus 5 (1M context) <noreply@anthropic.com>

docs/openontology-interoperability.md

@@ -68,15 +68,34 @@ Lookup works by exact id, canonical name, alias, or external id. `findEntities`
 
 `sameAs` is a reviewable claim, not an implicit merge. Two records only become one through an approved `merge-entity` operation, and the losing id survives as a redirect.
 
-## RDF, SHACL, OWL
+## RDF and Turtle
 
-Planned for a later phase, deliberately not faked in 0.1:
+```bash
+logicsrc ontology export --dir ./ethereum-ecosystem --format turtle --out graph.ttl
+```
 
-- **RDF/Turtle** — export and import of the losslessly mappable subset, using the same reified-claim shape as JSON-LD.
-- **SHACL** — the constraint kinds with genuinely equivalent semantics (`required-predicate`, `cardinality`, `unique`, `allowed-values`, `domain-range`) map to shapes. Query-based constraints do not, and will be reported as unmapped.
-- **OWL/RDFS** — an optional mapping for consumers needing formal reasoning. OpenOntology itself infers nothing: transitivity, symmetry, and inverses apply only when the schema declares them *and* a query asks.
+Claims are reified, exactly as in JSON-LD, and an **asserted relationship claim additionally emits the plain triple** — so a consumer that only wants the current accepted graph gets one without unpacking provenance.
 
-Until those ship, the compatibility matrix below says "planned", not "supported". Claiming compatibility that has not been implemented and tested is the thing this document exists to prevent.
+Import parses the profile this exporter produces rather than pretending to be a general Turtle parser. Anything it cannot interpret is listed in `unsupported`, never dropped silently.
+
+## SHACL
+
+```bash
+logicsrc ontology export --dir ./ethereum-ecosystem --format shacl --out shapes.ttl
+```
+
+Five constraint kinds map onto SHACL Core: `required-predicate`, `cardinality`, `allowed-values`, `domain-range`, and `temporal-bounds`. Severity carries across (`error` → `sh:Violation`, `warning` → `sh:Warning`).
+
+Two do **not**, and are reported as unmapped in the returned value *and* as comments in the generated Turtle:
+
+- `unique` — graph-wide uniqueness has no portable SHACL Core equivalent; it needs a `sh:SPARQLConstraint`.
+- `query` — an OpenOntology saved query is a triple-pattern AST, not SPARQL.
+
+A shape that silently means something narrower than the constraint it came from is worse than no shape, so those stay unmapped until the mapping is real.
+
+## OWL/RDFS
+
+Still planned. An optional mapping for consumers needing formal reasoning. OpenOntology itself infers nothing: transitivity, symmetry, and inverses apply only when the schema declares them *and* a query asks.
 
 ## Compatibility matrix
 
@@ -88,14 +107,18 @@ Until those ship, the compatibility matrix below says "planned", not "supported"
 | NDJSON | **supported** | Streaming entity/claim/source/evidence files |
 | JSON-LD 1.1 export | **supported** | Reified claims, PROV-O aliases, lossy report |
 | JSON-LD 1.1 import | **supported** | Round-trips the reference profile |
-| PROV-O | **partial** | Provenance terms aliased; full mapping later |
-| RDF / Turtle | planned | Phase 3 |
-| SHACL | planned | Phase 3, constraint subset only |
+| PROV-O | **partial** | Provenance terms aliased in JSON-LD and Turtle; full mapping later |
+| RDF / Turtle export | **supported** | Reified claims + plain triples for asserted relationships |
+| RDF / Turtle import | **supported** | Round-trips the reference profile; reports what it cannot read |
+| SHACL | **partial** | 5 of 7 constraint kinds; `unique` and `query` reported as unmapped |
 | OWL / RDFS | planned | Optional, for external reasoners |
 | SPARQL | planned | Query AST → SPARQL adapter |
 | Cypher | planned | Query AST → Cypher adapter |
 | Datalog | planned | Query AST → Datalog adapter |
-| SQLite / Turso | **supported** | Reference storage adapters |
+| SQLite / Turso | **supported** | `createLibsqlStore`, versioned migrations, FTS5 entity search |
+| REST + OpenAPI | **supported** | 16 paths, described at `/api/ontologies/openapi` |
+| Server-Sent Events | **supported** | Same event objects as the JSON endpoint |
+| MCP | **supported** | Resources, tools, and prompts; writes propose, never apply |
 | Neo4j / vector DBs | not required | Optional adapters; never mandatory |
 
 ## Query portability