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Refresh docs/arch/ to match current codebase (#5388)

The architecture docs had drifted since the v1beta1 graduation and the
migration of several packages into toolhive-core. This refresh
cross-references every claim against the current code in both repos and
brings the docs back in sync.

Highlights:
- Repoint moved packages: pkg/permissions, pkg/registry/types,
  pkg/registry/data/registry.json, secrets/aes key derivation, runtime
  monitor, and the registry-api manager
- Expand the operator CRD inventory: add EmbeddingServer (Auxiliary,
  StatefulSet) and MCPWebhookConfig; rename ToolConfig -> MCPToolConfig
- Fix CRD field paths: spec.config.compositeToolRefs;
  spec.incomingAuth.oidcConfigRef on VirtualMCPServer; MCPGroupRef
  consumers expanded to all four CRDs
- Rewrite vMCP middleware order to match server.go wrap order; correct
  Reporter interface naming; note logging reporter is Debug-level
- Add Cluster mode to the auth-server storage doc; flatten the
  timeouts CRD shape; fix sentinelTls casing; surface DCRCredentialStore
- Replace stale registry pieces: built-in catalog source, legacy
  top-level JSON examples, registry-API endpoint paths
  (/v0.1/servers, /v0.1/servers/:name/versions/latest), deprecation of
  thv group run
- Expand transport docs: NamedMiddleware constructor type; MCP env vars
  emitted only by pkg/runtime/setup.go; 127.0.0.1 default lives in the
  config builder; SSE rewrite in sse_response_processor.go
- Complete middleware enumeration in 02 and 05 (upstreamswap, awssts,
  obo, ratelimit, usagemetrics, recovery, header-forward, validating-
  webhook, mutating-webhook); fix authz -> authorization constant
- Restore pkg/secrets/types.go reference (EnvVarPrefix + Provider
  interface); point pod builder at pkg/controllerutil
- Skills: replace nonexistent skillsvc.go with real file inventory;
  add GET /content endpoint; mark oci_tags as reserved; correct OCI
  artifact name-match (last path component)
- Smaller fixes: Orb... (continued)

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