feat(openontology): implement OpenOntology Phase 0 + local engine and CLI (#99)

Implements OpenPRD 0001 through Phase 0 (specification, schemas, example,
docs surface) and Phase 1 (local engine, CLI, conformance tests).

Schemas (17 contracts, JSON Schema Draft 2020-12, additionalProperties:false)
  manifest, namespace, entity-type, property, relationship-type, constraint,
  query, action, entity, claim, source, evidence, changeset, review, approval,
  event, package — registered in @logicsrc/validators and exported from
  @logicsrc/schemas under https://logicsrc.com/schemas/openontology/.

@logicsrc/openontology
  - canonical JSON + sha256 package digests; YAML, JSON, NDJSON, and inline
    authoring all compile to the same bytes, so digests are authoring-agnostic
  - id profile: compact / IRI / urn with one canonicalization rule, prefix
    bound by a Namespace object so IRIs reverse unambiguously
  - validation: schema, graph (domain/range, datatypes, dangling refs),
    provenance (source-or-firstParty, agent runId, derivation inputs), policy
    (excerpt limits, licensing, visibility, staleness) and declared
    constraints; four severities, stable codes, text/json/yaml/markdown
  - portable triple-pattern query AST: multi-hop, 14 operators, asOf and
    recordedAsOf, per-status filtering, distinct/order/limit, explanation
    mode, and enforced depth/binding/row limits
  - append-only store: claims are immutable; dispute/retract/supersede append
    status transitions and the effective status is the latest one
  - change sets: 9 operations, atomic pre-flight, conflict detection on stale
    base revisions, semantic diff with duplicate-identity warnings and
    affected-query deltas, per-operation reviewer decisions
  - policy: agents propose but can never apply — the denial keys on actor
    type, so every scope plus high confidence plus --yolo still cannot apply;
    merges need approval, bulk retractions need two, undeclared action side
    effects are denied
  - JSON-LD 1.1 export/import with PROV-O aliases and lossy-field reporting
  - pluggable signature envelope with a jws-ed25519 reference profile and a
    fail-closed trust policy

CLI: logicsrc ontology init|validate|lint|build|inspect, entity, claim, query,
changeset, import, export, audit. Reads take --format, writes default to a
proposal, exit codes are stable for CI.

Example: examples/openontology/ethereum-ecosystem — 12 entity types, 17
relationship types, 63 entities, 169 claims, 25 sources, 31 evidence records,
5 saved queries, every claim lifecycle state, and a pending merge proposal.
All data is fictional; the directory is removable without affecting any core
test.

Docs: docs/openontology{,-governance,-interoperability}.md, a real
/openontology route, homepage + nav + sitemap entries, and a root README
section.

Verification: 112 new tests; full monorepo build and every workspace test
pass; conformance bundle (18 valid + 13 invalid fixtures) runs against the
published schemas alone; Node.js 25 and Bun 1.3 produce byte-identical
digests, revisions, event trails, and query results.

Not included (later PRD phases): MCP resources, REST/SSE, Turso adapter, TUI
and PWA surfaces, RDF/SHACL mappings, source adapters, governed actions.

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

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

examples/openontology/ethereum-ecosystem/schema/constraints.yaml

@@ -0,0 +1,43 @@
+- openontology: "0.1"
+  kind: Constraint
+  id: codebase-has-language
+  description: Every codebase should record its primary implementation language.
+  severity: info
+  remediation: Add a language claim for the codebase.
+  rule:
+    type: required-predicate
+    entityType: Codebase
+    predicate: language
+- openontology: "0.1"
+  kind: Constraint
+  id: layer2-settles-somewhere
+  description: Every layer 2 must declare the network it settles to.
+  severity: error
+  remediation: Add a deployedOn claim from the layer 2 to its base network.
+  rule:
+    type: cardinality
+    predicate: deployedOn
+    entityType: Layer2
+    min: 1
+    max: 1
+- openontology: "0.1"
+  kind: Constraint
+  id: chain-ids-unique
+  description: Two networks must not share a chain id.
+  severity: error
+  remediation: Correct the duplicated chainId claim.
+  rule:
+    type: unique
+    predicate: chainId
+- openontology: "0.1"
+  kind: Constraint
+  id: proof-system-known
+  description: A layer 2's proof system must be one of the three recognised kinds.
+  severity: error
+  rule:
+    type: allowed-values
+    predicate: proofSystem
+    values:
+      - validity
+      - fraud
+      - hybrid

examples/openontology/ethereum-ecosystem/schema/entity-types.yaml

@@ -0,0 +1,113 @@
+- openontology: "0.1"
+  kind: EntityType
+  id: Person
+  label: Person
+  description: A human participant in the ecosystem.
+  keyProperties:
+    - canonicalName
+  properties:
+    focus:
+      type: string
+      description: Primary area of work.
+    startedIn:
+      type: integer
+      description: Year they began working in the ecosystem.
+- openontology: "0.1"
+  kind: EntityType
+  id: Organization
+  label: Organization
+  description: A company, foundation, DAO, collective, or working group.
+  properties:
+    homepage:
+      type: url
+    kind:
+      type: enum
+      enum:
+        - company
+        - foundation
+        - dao
+        - collective
+- openontology: "0.1"
+  kind: EntityType
+  id: Project
+  label: Project
+  description: A named body of work people and organizations contribute to.
+  properties:
+    homepage:
+      type: url
+    startedOn:
+      type: date
+- openontology: "0.1"
+  kind: EntityType
+  id: Codebase
+  label: Codebase
+  description: A specific repository or source tree.
+  properties:
+    language:
+      type: string
+    license:
+      type: string
+    repository:
+      type: url
+- openontology: "0.1"
+  kind: EntityType
+  id: ResearchTopic
+  label: Research Topic
+  description: A research direction the ecosystem is actively working on.
+- openontology: "0.1"
+  kind: EntityType
+  id: Protocol
+  label: Protocol
+  description: A specified protocol or standard.
+  properties:
+    specification:
+      type: url
+- openontology: "0.1"
+  kind: EntityType
+  id: Network
+  label: Network
+  description: A live chain or network.
+  properties:
+    chainId:
+      type: integer
+- openontology: "0.1"
+  kind: EntityType
+  id: Layer2
+  label: Layer 2
+  description: A layer-2 network settling to a base layer.
+  properties:
+    proofSystem:
+      type: enum
+      enum:
+        - validity
+        - fraud
+        - hybrid
+- openontology: "0.1"
+  kind: EntityType
+  id: Application
+  label: Application
+  description: A user-facing application deployed on a network.
+- openontology: "0.1"
+  kind: EntityType
+  id: FundingProgram
+  label: Funding Program
+  description: A grants program, fund, or funding round.
+  properties:
+    budgetUsd:
+      type: number
+- openontology: "0.1"
+  kind: EntityType
+  id: Publication
+  label: Publication
+  description: A paper, spec, or long-form writeup.
+  properties:
+    published:
+      type: date
+- openontology: "0.1"
+  kind: EntityType
+  id: Event
+  label: Event
+  description: A conference, workshop, or summit.
+  properties:
+    held:
+      type: date

examples/openontology/ethereum-ecosystem/schema/namespaces.yaml

@@ -0,0 +1,5 @@
+- openontology: "0.1"
+  kind: Namespace
+  prefix: eth
+  uri: https://logicsrc.com/ontology/ethereum/
+  description: Compact id prefix for the Ethereum ecosystem example.

examples/openontology/ethereum-ecosystem/schema/properties.yaml

@@ -0,0 +1,84 @@
+- openontology: "0.1"
+  kind: Property
+  id: focus
+  label: focus
+  description: A person's primary area of work.
+  type: string
+- openontology: "0.1"
+  kind: Property
+  id: startedIn
+  label: startedIn
+  description: Year a person began working in the ecosystem.
+  type: integer
+- openontology: "0.1"
+  kind: Property
+  id: homepage
+  label: homepage
+  description: Canonical URL.
+  type: url
+- openontology: "0.1"
+  kind: Property
+  id: kind
+  label: kind
+  description: Organization kind.
+  type: string
+- openontology: "0.1"
+  kind: Property
+  id: startedOn
+  label: startedOn
+  description: Date a project began.
+  type: date
+- openontology: "0.1"
+  kind: Property
+  id: language
+  label: language
+  description: Primary implementation language of a codebase.
+  type: string
+- openontology: "0.1"
+  kind: Property
+  id: license
+  label: license
+  description: SPDX license of a codebase.
+  type: string
+- openontology: "0.1"
+  kind: Property
+  id: repository
+  label: repository
+  description: Repository URL.
+  type: url
+- openontology: "0.1"
+  kind: Property
+  id: specification
+  label: specification
+  description: Specification URL.
+  type: url
+- openontology: "0.1"
+  kind: Property
+  id: chainId
+  label: chainId
+  description: Network chain id.
+  type: integer
+- openontology: "0.1"
+  kind: Property
+  id: proofSystem
+  label: proofSystem
+  description: Layer-2 proof system.
+  type: string
+- openontology: "0.1"
+  kind: Property
+  id: budgetUsd
+  label: budgetUsd
+  description: Program budget in USD.
+  type: number
+- openontology: "0.1"
+  kind: Property
+  id: published
+  label: published
+  description: Publication date.
+  type: date
+- openontology: "0.1"
+  kind: Property
+  id: held
+  label: held
+  description: Event date.
+  type: date

examples/openontology/ethereum-ecosystem/schema/queries.yaml

@@ -0,0 +1,122 @@
+- openontology: "0.1"
+  kind: SavedQuery
+  id: people-working-on-topic
+  label: People and organizations working on a research topic
+  description: Every person working on a project that investigates the given research topic.
+  parameters:
+    topic:
+      type: string
+      required: true
+      default: eth:topic:zero-knowledge
+  query:
+    match:
+      - subject: ?person
+        predicate: worksOn
+        object: ?project
+      - subject: ?project
+        predicate: investigates
+        object: $topic
+    select:
+      - ?person
+      - ?project
+    include:
+      claimStatus:
+        - asserted
+      labels: true
+    orderBy:
+      - variable: ?person
+        direction: asc
+- openontology: "0.1"
+  kind: SavedQuery
+  id: codebases-implementing-protocol
+  label: Codebases implementing a protocol
+  description: Which codebases implement the given protocol, and who maintains them.
+  parameters:
+    protocol:
+      type: string
+      required: true
+      default: eth:protocol:proof-envelope
+  query:
+    match:
+      - subject: ?codebase
+        predicate: implements
+        object: $protocol
+      - subject: ?org
+        predicate: maintains
+        object: ?codebase
+    select:
+      - ?codebase
+      - ?org
+    include:
+      claimStatus:
+        - asserted
+      labels: true
+- openontology: "0.1"
+  kind: SavedQuery
+  id: orgs-behind-a-network
+  label: Organizations behind the codebases a network depends on
+  description: "Three hops: layer 2 → application → codebase → maintaining organization."
+  query:
+    match:
+      - subject: ?l2
+        predicate: deployedOn
+        object: ?network
+      - subject: ?app
+        predicate: runsOn
+        object: ?l2
+      - subject: ?app
+        predicate: uses
+        object: ?codebase
+      - subject: ?org
+        predicate: maintains
+        object: ?codebase
+    select:
+      - ?network
+      - ?l2
+      - ?app
+      - ?org
+    include:
+      claimStatus:
+        - asserted
+      labels: true
+    distinct: true
+- openontology: "0.1"
+  kind: SavedQuery
+  id: funded-work
+  label: Funded projects and research directions
+  description: Which funding programs support which projects or research topics.
+  query:
+    match:
+      - subject: ?fund
+        predicate: funds
+        object: ?target
+    select:
+      - ?fund
+      - ?target
+    include:
+      claimStatus:
+        - asserted
+      labels: true
+    orderBy:
+      - variable: ?fund
+        direction: asc
+- openontology: "0.1"
+  kind: SavedQuery
+  id: claims-needing-review
+  label: Claims that still need a human decision
+  description: Proposed and disputed claims, which a curator should accept, reject, or resolve.
+  query:
+    match:
+      - subject: ?subject
+        predicate: ?predicate
+        object: ?object
+        bindClaim: ?claim
+    select:
+      - ?claim
+      - ?subject
+      - ?predicate
+      - ?object
+    include:
+      claimStatus:
+        - proposed
+        - disputed

examples/openontology/ethereum-ecosystem/schema/relationships.yaml

@@ -0,0 +1,185 @@
+- openontology: "0.1"
+  kind: RelationshipType
+  id: worksAt
+  label: works at
+  description: A person is affiliated with an organization.
+  from:
+    - Person
+  to:
+    - Organization
+  cardinality: many-to-many
+  temporal: true
+- openontology: "0.1"
+  kind: RelationshipType
+  id: memberOf
+  label: member of
+  description: An organization belongs to a larger body.
+  from:
+    - Organization
+  to:
+    - Organization
+  cardinality: many-to-many
+  temporal: true
+- openontology: "0.1"
+  kind: RelationshipType
+  id: worksOn
+  label: works on
+  description: A person actively contributes work to a project.
+  from:
+    - Person
+  to:
+    - Project
+  cardinality: many-to-many
+  temporal: true
+  inverse: hasContributor
+- openontology: "0.1"
+  kind: RelationshipType
+  id: hasContributor
+  label: has contributor
+  description: Inverse of worksOn.
+  from:
+    - Project
+  to:
+    - Person
+  cardinality: many-to-many
+- openontology: "0.1"
+  kind: RelationshipType
+  id: contributesTo
+  label: contributes to
+  description: A person contributes to a codebase.
+  from:
+    - Person
+  to:
+    - Codebase
+  cardinality: many-to-many
+  temporal: true
+- openontology: "0.1"
+  kind: RelationshipType
+  id: maintains
+  label: maintains
+  description: An organization is responsible for a codebase.
+  from:
+    - Organization
+  to:
+    - Codebase
+  cardinality: many-to-many
+- openontology: "0.1"
+  kind: RelationshipType
+  id: builds
+  label: builds
+  description: An organization builds a project.
+  from:
+    - Organization
+  to:
+    - Project
+  cardinality: many-to-many
+  temporal: true
+- openontology: "0.1"
+  kind: RelationshipType
+  id: funds
+  label: funds
+  description: A funding program supports a project or research topic.
+  from:
+    - FundingProgram
+  to:
+    - Project
+    - ResearchTopic
+  cardinality: many-to-many
+  temporal: true
+- openontology: "0.1"
+  kind: RelationshipType
+  id: investigates
+  label: investigates
+  description: A project or person investigates a research topic.
+  from:
+    - Project
+    - Person
+    - Organization
+  to:
+    - ResearchTopic
+  cardinality: many-to-many
+  temporal: true
+- openontology: "0.1"
+  kind: RelationshipType
+  id: implements
+  label: implements
+  description: A codebase implements a protocol.
+  from:
+    - Codebase
+  to:
+    - Protocol
+  cardinality: many-to-many
+- openontology: "0.1"
+  kind: RelationshipType
+  id: uses
+  label: uses
+  description: A project or application uses a protocol or codebase.
+  from:
+    - Project
+    - Application
+  to:
+    - Protocol
+    - Codebase
+  cardinality: many-to-many
+- openontology: "0.1"
+  kind: RelationshipType
+  id: runsOn
+  label: runs on
+  description: An application runs on a network or layer 2.
+  from:
+    - Application
+  to:
+    - Network
+    - Layer2
+  cardinality: many-to-many
+- openontology: "0.1"
+  kind: RelationshipType
+  id: deployedOn
+  label: deployed on
+  description: A layer 2 settles to a base network.
+  from:
+    - Layer2
+  to:
+    - Network
+  cardinality: many-to-many
+- openontology: "0.1"
+  kind: RelationshipType
+  id: dependsOn
+  label: depends on
+  description: A codebase depends on another codebase.
+  from:
+    - Codebase
+  to:
+    - Codebase
+  cardinality: many-to-many
+- openontology: "0.1"
+  kind: RelationshipType
+  id: authored
+  label: authored
+  description: A person authored a publication.
+  from:
+    - Person
+  to:
+    - Publication
+  cardinality: many-to-many
+- openontology: "0.1"
+  kind: RelationshipType
+  id: collaboratesWith
+  label: collaborates with
+  description: Two people work together.
+  from:
+    - Person
+  to:
+    - Person
+  cardinality: many-to-many
+  symmetric: true
+- openontology: "0.1"
+  kind: RelationshipType
+  id: forkedFrom
+  label: forked from
+  description: A codebase was forked from another.
+  from:
+    - Codebase
+  to:
+    - Codebase
+  cardinality: many-to-many