Update docs for v1beta1 CRD stabilization epic

[ChrisJBurns]

Summary

The v1beta1 CRD stabilization epic (stacklok/stacklok-epics#291) introduced several new features and breaking changes across 7 closed tickets (#4247, #4248, #4249, #4250, #4252, #4267, #4275), but the in-repo documentation was not updated to reflect them. This PR brings all documentation, examples, and architecture diagrams up to date.

Type of change

• Documentation update

Changes

File	Change
docs/arch/09-operator-architecture.md	Added MCPOIDCConfig + MCPTelemetryConfig to CRD overview diagram, layer table, logical CRD table, and mermaid relationship chart. Added dedicated sections for both new CRDs. Updated MCPServer and MCPRemoteProxy sections with new ref fields and deprecation notes. Fixed stale port: → proxyPort: in YAML example. Rewrote Configuration References to lead with shared CRD pattern.
docs/operator/virtualmcpserver-api.md	Documented oidcConfigRef field in .spec.incomingAuth with full field descriptions. Added deprecation notice on inline oidcConfig. Added preferred YAML example with MCPOIDCConfig. Documented oidcConfigHash status field. Added MCPOIDCConfig to Related Resources.
docs/observability.md	Added MCPTelemetryConfig CRD section with inline YAML example as the preferred Kubernetes pattern. Marked inline spec.openTelemetry as deprecated.
docs/operator/virtualmcpserver-kubernetes-guide.md	Updated OIDC migration scenario to recommend oidcConfigRef with MCPOIDCConfig. Added hint in VirtualMCPServer creation example.
examples/operator/mcp-servers/mcpserver_with_oidcconfig_ref.yaml	New. MCPOIDCConfig (both K8s SA and inline variants) + MCPServer with oidcConfigRef.
examples/operator/mcp-servers/mcpremoteproxy_with_oidcconfig_ref.yaml	New. MCPOIDCConfig + MCPRemoteProxy with oidcConfigRef.
examples/operator/virtual-mcps/vmcp_with_oidcconfig_ref.yaml	New. MCPOIDCConfig + VirtualMCPServer with oidcConfigRef in incomingAuth.
5 existing example YAMLs	Added deprecation header comments pointing to the new *_oidcconfig_ref.yaml examples.

Test plan

• Verified all modified markdown renders correctly (headings, tables, YAML blocks, mermaid diagrams)
• Verified new example YAMLs use correct field names matching current CRD types
• Verified no references to removed fields (port, targetPort, toolsFilter, clientSecret, thvCABundlePath) remain in updated docs
• Cross-referenced field names against cmd/thv-operator/api/v1alpha1/ type definitions

Special notes for reviewers

This is a docs-only PR covering the closed tickets from the CRD stabilization epic. The 3 still-open tickets (#4251 MCPRegistry status consolidation, #4253 workload CRD config reference updates, #4254 MCPRemoteEndpoint) will need additional doc updates when they land.

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[ChrisJBurns]

@claude Please use the agents to ensure this PR has documentation that is correct. Please use the docs review skill also.

[claude]

Claude finished @ChrisJBurns's task in 6m 4s —— View job

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Documentation Review Complete

• Gather context: read changed files and CRD type definitions
• Run doc-review skill against changed documentation files
• Fix critical bugs found in YAML examples
• Fix complete example in virtualmcpserver-api.md
• Report all findings

---

Findings and Fixes Applied

Two critical bugs and one misleading example were found and fixed in commit 8e4d900.

Bug 1 — upstreamURL instead of remoteURL (Critical) ✅ Fixed

Files: mcpremoteproxy_with_oidcconfig_ref.yaml (new), mcpremoteproxy_with_inline_oidc_secretref.yaml (modified)

The MCPRemoteProxySpec Go type defines the required URL field as json:"remoteURL". Both example files used upstreamURL, which is an unknown field that Kubernetes would silently prune — leaving the required remoteURL field absent and causing API validation failure. All other docs and the existing crd-api.md correctly use remoteURL.

# Before (broken — field pruned by API server)
spec:
  upstreamURL: "https://api.github.com/mcp"

# After (correct)
spec:
  remoteURL: "https://api.github.com/mcp"

Bug 2 — audience set on kubernetesServiceAccount (invalid field) ✅ Fixed

Files: mcpserver_with_oidcconfig_ref.yaml, mcpremoteproxy_with_oidcconfig_ref.yaml

KubernetesServiceAccountOIDCConfig has no audience field — by design, since the CRD comment explicitly states it contains "shared fields without audience, which is specified per-server via MCPOIDCConfigReference." The audience belongs on oidcConfigRef.audience, not on the shared MCPOIDCConfig. The Kubernetes API server would silently prune this field, meaning the intended value was never actually set.

# Before (audience silently pruned — wrong location)
spec:
  type: kubernetesServiceAccount
  kubernetesServiceAccount:
    audience: toolhive

# After (correct — empty is valid; audience goes on oidcConfigRef instead)
  # serviceAccount and namespace default to the pod's own SA and namespace
  kubernetesServiceAccount: {}

Warning 1 — Complete example used deprecated oidcConfig form ✅ Fixed

File: docs/operator/virtualmcpserver-api.md complete example (lines 463–478)

The PR correctly documented oidcConfigRef as the preferred pattern and deprecated oidcConfig, but the "Complete Example" at the bottom of the file — the most prominent copy-paste reference — still used the deprecated form. Updated to use oidcConfigRef.

---

Pre-existing Issues (Not Introduced by This PR)

These were found during review but pre-date this PR. Flagging for awareness:

	File	Issue
⚠️	virtualmcpserver-api.md line ~487	outgoingAuth.backends.slack.type: service_account is not a valid enum value (discovered and external_auth_config_ref are the only valid values per CRD markers)
⚠️	virtualmcpserver-api.md lines 390–400	status.capabilities and status.observedGeneration documented but don't exist in VirtualMCPServerStatus Go type
💡	virtualmcpserver-api.md line 595	Related Resources links MCPOIDCConfig to a YAML example file rather than the API reference (crd-api.md)

These are outside the scope of this PR but worth tracking as follow-up issues.

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Documentation Quality: Good

The overall documentation is well-structured and thorough. The deprecation notices are consistently placed, the mermaid diagrams and CRD layer diagrams correctly reflect the new CRDs, and the field descriptions match the Go types (after the above fixes). The new example YAML files follow the namespace conventions and clearly explain the preferred patterns.
| Branch

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 68.86%. Comparing base (bd4a04f) to head (1255e44).
⚠️ Report is 4 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #4536      +/-   ##
==========================================
+ Coverage   68.85%   68.86%   +0.01%     
==========================================
  Files         505      505              
  Lines       52318    52378      +60     
==========================================
+ Hits        36022    36069      +47     
- Misses      13506    13520      +14     
+ Partials     2790     2789       -1     

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