Merge branch 'main' into fix-connectivity-panic

Author: SamMorrowDrums

.github/pull_request_template.md

@@ -33,6 +33,13 @@ Fixes #
 - [ ] Auth / permissions considered
 - [ ] Data exposure, filtering, or token/size limits considered
 
+## Tool renaming
+- [ ] I am renaming tools as part of this PR (e.g. a part of a consolidation effort)
+   - [ ] I have added the new tool aliases in `deprecated_tool_aliases.go` 
+- [ ] I am not renaming tools as part of this PR
+
+Note: if you're renaming tools, you *must* add the tool aliases. For more information on how to do so, please refer to the [official docs](https://github.com/github/github-mcp-server/blob/main/docs/tool-renaming.md).
+
 ## Lint & tests
 <!-- Check what you ran. If not run, explain briefly. -->
 - [ ] Linted locally with `./script/lint`

.github/workflows/code-scanning.yml

@@ -14,6 +14,8 @@ env:
 jobs:
   analyze:
     name: Analyze (${{ matrix.language }})
+    # Only run on the main repository, not on forks
+    if: github.repository == 'github/github-mcp-server'
     runs-on: ${{ fromJSON(matrix.runner) }}
     permissions:
       actions: read

.github/workflows/docker-publish.yml

@@ -70,7 +70,7 @@ jobs:
       # https://github.com/docker/metadata-action
       - name: Extract Docker metadata
         id: meta
-        uses: docker/metadata-action@318604b99e75e41977312d83839a89be02ca4893 # v5.9.0
+        uses: docker/metadata-action@c299e40c65443455700f0fdfc63efafe5b349051 # v5.10.0
         with:
           images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
           tags: |

.github/workflows/license-check.yml

@@ -25,8 +25,12 @@ jobs:
     steps:
       - name: Check out code
         uses: actions/checkout@v6
-        with:
-          ref: ${{ github.head_ref }}
+
+      # Check out the actual PR branch so we can push changes back if needed
+      - name: Check out PR branch
+        env:
+          GH_TOKEN: ${{ github.token }}
+        run: gh pr checkout ${{ github.event.pull_request.number }}
 
       - name: Set up Go
         uses: actions/setup-go@v6
@@ -57,15 +61,13 @@ jobs:
           git config user.name "github-actions[bot]"
           git config user.email "github-actions[bot]@users.noreply.github.com"
           git add third-party-licenses.*.md third-party/
-          git commit -m "chore: regenerate license files
-
-Auto-generated by license-check workflow"
+          git commit -m "chore: regenerate license files" -m "Auto-generated by license-check workflow"
           git push
 
       - name: Check if already commented
         if: steps.changes.outcome == 'failure' && steps.push.outcome == 'failure'
         id: check_comment
-        uses: actions/github-script@v7
+        uses: actions/github-script@v8
         with:
           script: |
             const { data: comments } = await github.rest.issues.listComments({
@@ -83,26 +85,26 @@ Auto-generated by license-check workflow"
 
       - name: Comment with instructions if cannot push
         if: steps.changes.outcome == 'failure' && steps.push.outcome == 'failure' && steps.check_comment.outputs.already_commented == 'false'
-        uses: actions/github-script@v7
+        uses: actions/github-script@v8
         with:
           script: |
             await github.rest.issues.createComment({
               owner: context.repo.owner,
               repo: context.repo.repo,
               issue_number: context.issue.number,
               body: `## ⚠️ License files need updating
-
-The license files are out of date. I tried to fix them automatically but don't have permission to push to this branch.
-
-**Please run:**
-\`\`\`bash
-script/licenses
-git add third-party-licenses.*.md third-party/
-git commit -m "chore: regenerate license files"
-git push
-\`\`\`
-
-Alternatively, enable "Allow edits by maintainers" in the PR settings so I can fix it automatically.`
+            
+            The license files are out of date. I tried to fix them automatically but don't have permission to push to this branch.
+            
+            **Please run:**
+            \`\`\`bash
+            script/licenses
+            git add third-party-licenses.*.md third-party/
+            git commit -m "chore: regenerate license files"
+            git push
+            \`\`\`
+            
+            Alternatively, enable "Allow edits by maintainers" in the PR settings so I can fix it automatically.`
             });
 
       - name: Fail check if changes needed

README.md

@@ -1,6 +1,7 @@
 package main
 
 import (
+	"context"
 	"fmt"
 	"net/url"
 	"os"
@@ -11,7 +12,6 @@ import (
 	"github.com/github/github-mcp-server/pkg/inventory"
 	"github.com/github/github-mcp-server/pkg/translations"
 	"github.com/google/jsonschema-go/jsonschema"
-	"github.com/modelcontextprotocol/go-sdk/mcp"
 	"github.com/spf13/cobra"
 )
 
@@ -50,8 +50,8 @@ func generateReadmeDocs(readmePath string) error {
 	// Create translation helper
 	t, _ := translations.TranslationHelper()
 
-	// Build inventory - stateless, no dependencies needed for doc generation
-	r := github.NewInventory(t).Build()
+	// (not available to regular users) while including tools with FeatureFlagDisable.
+	r := github.NewInventory(t).WithToolsets([]string{"all"}).Build()
 
 	// Generate toolsets documentation
 	toolsetsDoc := generateToolsetsDoc(r)
@@ -153,9 +153,7 @@ func generateToolsetsDoc(i *inventory.Inventory) string {
 }
 
 func generateToolsDoc(r *inventory.Inventory) string {
-	// AllTools() returns tools sorted by toolset ID then tool name.
-	// We iterate once, grouping by toolset as we encounter them.
-	tools := r.AllTools()
+	tools := r.AvailableTools(context.Background())
 	if len(tools) == 0 {
 		return ""
 	}
@@ -190,7 +188,7 @@ func generateToolsDoc(r *inventory.Inventory) string {
 			currentToolsetID = tool.Toolset.ID
 			currentToolsetIcon = tool.Toolset.Icon
 		}
-		writeToolDoc(&toolBuf, tool.Tool)
+		writeToolDoc(&toolBuf, tool)
 		toolBuf.WriteString("\n\n")
 	}
 
@@ -200,40 +198,26 @@ func generateToolsDoc(r *inventory.Inventory) string {
 	return buf.String()
 }
 
-func formatToolsetName(name string) string {
-	switch name {
-	case "pull_requests":
-		return "Pull Requests"
-	case "repos":
-		return "Repositories"
-	case "code_security":
-		return "Code Security"
-	case "secret_protection":
-		return "Secret Protection"
-	case "orgs":
-		return "Organizations"
-	default:
-		// Fallback: capitalize first letter and replace underscores with spaces
-		parts := strings.Split(name, "_")
-		for i, part := range parts {
-			if len(part) > 0 {
-				parts[i] = strings.ToUpper(string(part[0])) + part[1:]
-			}
+func writeToolDoc(buf *strings.Builder, tool inventory.ServerTool) {
+	// Tool name (no icon - section header already has the toolset icon)
+	fmt.Fprintf(buf, "- **%s** - %s\n", tool.Tool.Name, tool.Tool.Annotations.Title)
+
+	// OAuth scopes if present
+	if len(tool.RequiredScopes) > 0 {
+		fmt.Fprintf(buf, "  - **Required OAuth Scopes**: `%s`\n", strings.Join(tool.RequiredScopes, "`, `"))
+
+		// Only show accepted scopes if they differ from required scopes
+		if len(tool.AcceptedScopes) > 0 && !scopesEqual(tool.RequiredScopes, tool.AcceptedScopes) {
+			fmt.Fprintf(buf, "  - **Accepted OAuth Scopes**: `%s`\n", strings.Join(tool.AcceptedScopes, "`, `"))
 		}
-		return strings.Join(parts, " ")
 	}
-}
-
-func writeToolDoc(buf *strings.Builder, tool mcp.Tool) {
-	// Tool name (no icon - section header already has the toolset icon)
-	fmt.Fprintf(buf, "- **%s** - %s\n", tool.Name, tool.Annotations.Title)
 
 	// Parameters
-	if tool.InputSchema == nil {
+	if tool.Tool.InputSchema == nil {
 		buf.WriteString("  - No parameters required")
 		return
 	}
-	schema, ok := tool.InputSchema.(*jsonschema.Schema)
+	schema, ok := tool.Tool.InputSchema.(*jsonschema.Schema)
 	if !ok || schema == nil {
 		buf.WriteString("  - No parameters required")
 		return
@@ -282,6 +266,28 @@ func writeToolDoc(buf *strings.Builder, tool mcp.Tool) {
 	}
 }
 
+// scopesEqual checks if two scope slices contain the same elements (order-independent)
+func scopesEqual(a, b []string) bool {
+	if len(a) != len(b) {
+		return false
+	}
+
+	// Create a map for quick lookup
+	aMap := make(map[string]bool, len(a))
+	for _, scope := range a {
+		aMap[scope] = true
+	}
+
+	// Check if all elements in b are in a
+	for _, scope := range b {
+		if !aMap[scope] {
+			return false
+		}
+	}
+
+	return true
+}
+
 func contains(slice []string, item string) bool {
 	for _, s := range slice {
 		if s == item {

cmd/github-mcp-server/generate_docs.go

@@ -0,0 +1,29 @@
+package main
+
+import "strings"
+
+// formatToolsetName converts a toolset ID to a human-readable name.
+// Used by both generate_docs.go and list_scopes.go for consistent formatting.
+func formatToolsetName(name string) string {
+	switch name {
+	case "pull_requests":
+		return "Pull Requests"
+	case "repos":
+		return "Repositories"
+	case "code_security":
+		return "Code Security"
+	case "secret_protection":
+		return "Secret Protection"
+	case "orgs":
+		return "Organizations"
+	default:
+		// Fallback: capitalize first letter and replace underscores with spaces
+		parts := strings.Split(name, "_")
+		for i, part := range parts {
+			if len(part) > 0 {
+				parts[i] = strings.ToUpper(string(part[0])) + part[1:]
+			}
+		}
+		return strings.Join(parts, " ")
+	}
+}