The Plugin and NativeExtension NodeKinds enumerate containsskill, containssubagent, containstoolserver edges. There is no representation of:

The pricing typo by itself makes derived cost calculations wrong by 3000x. P0.

schema/examples/compute/mcp-transports/streamable-http.yaml records specVersion: "2025-03-26". The MCPTransport NodeKind only carries kind/specUrl/specVersion. There is no enumeration of MCP spec revisions, and no notion of feature deltas across revisions (e.g. elicitation, structured tool output, resource links, OAuth Resource Server classification, removal of JSON-RPC batching, mandatory MCP-Protocol-Version header).

ModelVersion.supportsThinking: bool + thinkingEffortLevels + supportsThinkingBudgetTokens. Anthropic now ships TWO distinct thinking modes:

Skill NodeKind has one shape: directory-of-markdown with SKILL.md entrypoint. Anthropic now ships TWO distinct concepts both called "Skill":

schema/examples/agent-stack/products/cursor.yaml is a 16-line stub. schema/examples/agent-stack/capability-profiles/cursor-default.yaml and cursor-cli-permissive.yaml exist but the CapabilityProfile NodeKind only carries default, description, overrides — it cannot express Cursor's mode taxonomy:

ToolDescriptor and ToolServer NodeKinds describe a tool's name, schema, and protocol but do not represent:

Provider.authMethods enumerates api-key,oauth,browser-login,service-account,iam,device-code. ToolServer has no auth attribute at all. The 2025-06-18 MCP revision classifies MCP servers as OAuth Resource Servers (RFC 6749 §1.4) and requires clients to implement Resource Indicators (RFC 8707) to prevent token-theft attacks. The schema cannot express any of this.

The repo's live packages/agent-catalog/graph/schema/ontology-schema.yaml defines DiscoverySignal (with signalKind, key, matchMode, confidence, argvMatches, etc.) and a discoveredby edge. v6 graph treats discovery as out-of-scope ("Discovery runtime queries (detectHostAgent, listInstalledAgents)... runtime API; the catalog describes the data such queries consume; the queries themselves are not schema").

The repo defines two per-AgentVersion semantics nodes:

Lower-impact catalog completeness gap.

MCPTransport.kind: enum<stdio,streamable-http,sse,websocket>. Coverage-checklist row says HTTP+SSE is "deprecated" and WebSocket is "community" / not-in-spec, but the schema has no status attribute on MCPTransport. Examples show status: live only for streamable-http, but the field isn't in the NodeKind definition (only in the example).

Lower priority than Anthropic gaps because Codex's surface evolves slower, but coverage parity matters.

Repo defines:

Repo has PluginArtifact (artifactKind, pathPattern, installerSurface) emitted via PluginTarget emitsartifact PluginArtifact. v6 schema has NativeExtension/PortableExtension/Plugin but no concept of the physical artifact files a plugin compiles to.

schema/examples/benchmarks/ directory absent or sparse. Coverage-checklist OpenQuestion "Benchmark-run primitives at SDK layer" is unresolved. Major 2025/2026 benchmarks not represented:

coverage-checklist.md references PathDescriptor in at least 4 rows ("Run dir layout PathDescriptor per file", "PathDescriptor for ~/.a5c/", "Layout version", others). It is NOT present in schema/ontology-schema.yaml nodeKinds: list (verified by grep). It is NOT in 02-node-kinds/README.md cluster table. The repo agent-catalog DOES define PathDescriptor. So the v6 schema cites a NodeKind that does not exist.

ontology-schema.yaml lists ~115 edges (e.g. applies-to, composes-stack, delegated-from, phase-in, compiled-from, closed-by, compiles-to, compiled-from, discovered-by, evidenceSource attrustlevel...).

ontology-schema.yaml defines MCPTransport with attributes: id, displayName, kind, specUrl. The example streamable-http.yaml uses two extra fields: specVersion: "2025-03-26" and status: live. These are not declared in the NodeKind. This breaks V-12.5 (NodeKind ↔ examples must be consistent).

02-node-kinds/README.md line 8 declares: "The schema is organized into 15 clusters." File listing shows 13 sibling .md files (agent-stack, benchmarks, capabilities, catalog-meta, channels-hooks, domain-ontology, extensions-plugins, lifecycle, role-ontology, sourceref-and-scope, stack-layers, terminology, transport, trust). README cluster index needs to list 15 clusters with their NodeKind tables; appears to enumerate 12-13.

Beyond PathDescriptor (its own gap), coverage-checklist mentions:

ModelVersion.versionRange: versionRange semantically conflates "this version" with "a range of versions". Example claude-opus-4-7.yaml has versionRange: ">=4.7.0 <5.0.0" which is a range, but model:claude-opus-4-7 is intended to be one specific snapshot (claude-opus-4-7-20251201 or similar). The repo agent-catalog distinguishes ModelFamily (range-bearing) from ModelVersion (concrete snapshot id).