feat(toolhive): re-enable the GitHub MCP over streamable-http

[Tanguille]

Re-enables the GitHub MCP server, disabled since ToolHive v0.40.1 health monitoring re-ran initialize against its stdio backend and degraded the resources and unified gateways (upstream #5890).

Why a transport change, not a different server

Question	Answer
Is there a newer toolhive that fixes it?	No. v0.40.1 is latest (released 2026-07-20) and is what we pin. Issue #5890 is open, untriaged, zero linked PRs
Does the same server support HTTP?	Yes, since PR #1849. Read-only enforcement in HTTP mode was broken at first and fixed by #2208, in every release from v1.0.0
Better alternative?	No. octocode-mcp is stdio-only with no container image; Docker Hub mcp/github wraps the archived implementation, stdio-only, latest tag only

The part the transport change forces

http takes no server-side token. Unlike the stdio path, its ServerConfig has no Token field and it authenticates per request, so the PAT cannot stay an env var:

// cmd/github-mcp-server/main.go - stdio
stdioServerConfig := ghmcp.StdioServerConfig{ ... Token: token, ... }
// http - no Token field anywhere in httpConfig

So the PAT moves to an MCPExternalAuthConfig of type bearerToken, which makes the proxy attach it as an Authorization header. This is the first MCPExternalAuthConfig in the cluster.

Scoping

--read-only plus --toolsets context,repos,issues,pull_requests. The full server exposes ~79 tools and every one lands in the unified gateway's semantic tool index. No MCPToolConfig: toolsFilter: [] is a proven no-op (see #4211), so scoping is done on the server itself.

Verified

• ghcr.io/github/github-mcp-server:v1.7.0 manifest exists on ghcr (amd64+arm64), released 2026-07-23
• all three objects pass kubectl apply --dry-run=server
• toolhive-secrets still carries GITHUB_PERSONAL_ACCESS_TOKEN

Not runtime-verified — no pods have been started. Draft until someone watches the first rollout: confirm the pod goes Ready, github_* tools appear on vmcp-resources, and the unified gateway does not report a degraded backend.

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📥 Commits

Reviewing files that changed from the base of the PR and between 7f352ce and 73cca9b.

📒 Files selected for processing (1)

• kubernetes/apps/ai/toolhive/config/github.yaml

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch feat/github-mcp-http

---

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[tanguille-cluster]

@@ (root level) @@
# toolhive.stacklok.dev/v1beta1/MCPToolConfig/ai/github
! - one document removed:
- apiVersion: toolhive.stacklok.dev/v1beta1
- kind: MCPToolConfig
- metadata:
-   name: github
-   namespace: ai
-   labels:
-     app.kubernetes.io/name: toolhive
-     kustomize.toolkit.fluxcd.io/name: toolhive
-     kustomize.toolkit.fluxcd.io/namespace: ai
- spec:
-   toolsFilter: []

@@ (root level) @@
# toolhive.stacklok.dev/v1beta1/MCPExternalAuthConfig/ai/github
! + one document added:
+ apiVersion: toolhive.stacklok.dev/v1beta1
+ kind: MCPExternalAuthConfig
+ metadata:
+   name: github
+   namespace: ai
+   labels:
+     app.kubernetes.io/name: toolhive
+     kustomize.toolkit.fluxcd.io/name: toolhive
+     kustomize.toolkit.fluxcd.io/namespace: ai
+ spec:
+   type: bearerToken
+   bearerToken:
+     tokenSecretRef:
+       name: toolhive-secrets
+       key: GITHUB_PERSONAL_ACCESS_TOKEN

@@ (root level) @@
# toolhive.stacklok.dev/v1beta1/MCPServer/ai/github
! + one document added:
+ apiVersion: toolhive.stacklok.dev/v1beta1
+ kind: MCPServer
+ metadata:
+   name: github
+   namespace: ai
+   labels:
+     app.kubernetes.io/name: toolhive
+     kustomize.toolkit.fluxcd.io/name: toolhive
+     kustomize.toolkit.fluxcd.io/namespace: ai
+ spec:
+   resources:
+     limits:
+       cpu: 200m
+       memory: 200Mi
+     requests:
+       cpu: 10m
+       memory: 64Mi
+   image: "ghcr.io/github/github-mcp-server:v1.7.0"
+   mcpPort: 8082
+   proxyPort: 8080
+   transport: streamable-http
+   args:
+   - http
+   - "--read-only"
+   - "--toolsets"
+   - "context,repos,issues,pull_requests"
+   externalAuthConfigRef:
+     name: github
+   groupRef:
+     name: resources
+   permissionProfile:
+     name: network
+     type: builtin
+   podTemplateSpec:
+     spec:
+       containers:
+       - name: mcp
+         resources:
+           limits:
+             cpu: 500m
+             memory: 256Mi
+           requests:
+             cpu: 10m
+             memory: 64Mi

@@ (root level) @@
# toolhive.stacklok.dev/v1beta1/MCPServer/ai/github-opt
! + one document added:
+ apiVersion: toolhive.stacklok.dev/v1beta1
+ kind: MCPServer
+ metadata:
+   name: github-opt
+   namespace: ai
+   labels:
+     app.kubernetes.io/name: toolhive
+     kustomize.toolkit.fluxcd.io/name: toolhive
+     kustomize.toolkit.fluxcd.io/namespace: ai
+ spec:
+   resources:
+     limits:
+       cpu: 200m
+       memory: 200Mi
+     requests:
+       cpu: 10m
+       memory: 64Mi
+   image: "ghcr.io/github/github-mcp-server:v1.7.0"
+   mcpPort: 8082
+   proxyPort: 8080
+   transport: streamable-http
+   args:
+   - http
+   - "--read-only"
+   - "--toolsets"
+   - "context,repos,issues,pull_requests"
+   externalAuthConfigRef:
+     name: github
+   groupRef:
+     name: all
+   permissionProfile:
+     name: network
+     type: builtin
+   podTemplateSpec:
+     spec:
+       containers:
+       - name: mcp
+         resources:
+           limits:
+             cpu: 500m
+             memory: 256Mi
+           requests:
+             cpu: 10m
+             memory: 64Mi

[github-actions]

AI Automated Review

Analysis engine: qwen-3.6-fast@http://litellm.ai.svc.cluster.local/v1 (openai)

Recommendation: Approve

This PR cleanly re-enables the GitHub MCP server by switching from stdio to streamable-http transport, addressing the upstream health-check initialization bug (PR 5890). The implementation correctly handles the authentication model change (moving PAT to MCPExternalAuthConfig) and updates the image version.

Change-by-Change Findings

1. Transport & Auth Refactor:

   • Switched transport from stdio to streamable-http for both github and github-opt servers.
   • Introduced MCPExternalAuthConfig named github with type: bearerToken. This is required because the HTTP mode does not accept a token via env vars like stdio did; instead, it relies on the proxy injecting an Authorization header.
   • Verified that externalAuthConfigRef is set on both MCPServer objects.
   • Confirmed toolhive-secrets contains GITHUB_PERSONAL_ACCESS_TOKEN (per PR body).

2. Image Version Bump:

   • Updated ghcr.io/github/github-mcp-server from v1.6.0 to v1.7.0.
   • v1.7.0 includes MCP spec updates (go-sdk 1.7.0-pre.3) and lockdown improvements. No breaking changes identified in release notes that affect this configuration.

3. Scoping & Args:

   • Added --read-only and --toolsets context,repos,issues,pull_requests args. This aligns with the PR description's intent to limit tool exposure (~79 tools total) and keep the optimizer index small.
   • Removed MCPToolConfig reference as noted in PR body (toolsFilter: [] is a no-op).

4. Resources & Ports:

   • Set mcpPort: 8082 and proxyPort: 8080, matching default HTTP bindings.
   • Resource requests/limits remain unchanged from the commented-out stdio config, which is appropriate.

Standards Compliance

• YAML Structure: Follows repository conventions for ToolHive manifests. Uses schema annotations.
• Secrets Handling: Does not commit secrets; references existing SOPS-managed secret toolhive-secrets. Complies with AGENTS.md safety rules.
• Commit Title: feat(toolhive): ... follows Conventional Commits.

Release Notes (github-mcp-server v1.7.0)

• Server-to-server auth support for GitHub apps (stdio).
• Projects tools pagination improved.
• MCP 2026-07-28 spec compliance via go-sdk 1.7.0-pre.3.
• Lockdown mode improvements.
• Various dependency bumps (go-chi, docker actions, golang, distroless).

Unknowns / Needs Verification

• Runtime Validation: As noted in the PR body, this has not been runtime-verified. Ensure pods become Ready and tools appear in the unified gateway after merge.
• Schema Availability: The $schema URLs (k8s-schemas.home-operations.com) were not fetchable during review but are standard for this repo. Assume valid per repo history.