Merge branch 'main' of https://github.com/github/github-mcp-server

* 'main' of https://github.com/github/github-mcp-server:
  Add Gemini CLI extension (github#1232)
  Adding default toolset as configuration (github#1229)

Author: pohi99999

README.md

@@ -87,17 +87,12 @@ Alternatively, to manually configure VS Code, choose the appropriate JSON block
 
 ### Configuration
 
-#### Default toolset configuration
-
-The default configuration is:
-- context
-- repos
-- issues
-- pull_requests
-- users
+#### Toolset configuration
 
 See [Remote Server Documentation](docs/remote-server.md) for full details on remote server configuration, toolsets, headers, and advanced usage. This file provides comprehensive instructions and examples for connecting, customizing, and installing the remote GitHub MCP Server in VS Code and other MCP hosts.
 
+When no toolsets are specified, [default toolsets](#default-toolset) are used.
+
 #### Enterprise Cloud with data residency (ghe.com)
 
 GitHub Enterprise Cloud can also make use of the remote server.
@@ -329,7 +324,7 @@ The GitHub MCP Server supports enabling or disabling specific groups of function
 
 _Toolsets are not limited to Tools. Relevant MCP Resources and Prompts are also included where applicable._
 
-The Local GitHub MCP Server follows the same [default toolset configuration](#default-toolset-configuration) as the remote version.
+When no toolsets are specified, [default toolsets](#default-toolset) are used.
 
 #### Specifying Toolsets
 
@@ -359,7 +354,9 @@ docker run -i --rm \
   ghcr.io/github/github-mcp-server
 ```
 
-### The "all" Toolset
+### Special toolsets
+
+#### "all" toolset
 
 The special toolset `all` can be provided to enable all available toolsets regardless of any other configuration:
 
@@ -373,6 +370,22 @@ Or using the environment variable:
 GITHUB_TOOLSETS="all" ./github-mcp-server
 ```
 
+#### "default" toolset
+The default toolset `default` is the configuration that gets passed to the server if no toolsets are specified.
+
+The default configuration is:
+- context
+- repos
+- issues
+- pull_requests
+- users
+
+To keep the default configuration and add additional toolsets:
+
+```bash
+GITHUB_TOOLSETS="default,stargazers" ./github-mcp-server
+```
+
 ### Available Toolsets
 
 The following sets of tools are available:

cmd/github-mcp-server/main.go

@@ -45,8 +45,9 @@ var (
 				return fmt.Errorf("failed to unmarshal toolsets: %w", err)
 			}
 
+			// No passed toolsets configuration means we enable the default toolset
 			if len(enabledToolsets) == 0 {
-				enabledToolsets = github.GetDefaultToolsetIDs()
+				enabledToolsets = []string{github.ToolsetMetadataDefault.ID}
 			}
 
 			stdioServerConfig := ghmcp.StdioServerConfig{

docs/installation-guides/install-gemini-cli.md

@@ -14,7 +14,7 @@ For security, avoid hardcoding your token. Create or update `~/.gemini/.env` (wh
 
 ```bash
 # ~/.gemini/.env
-GITHUB_PAT=your_token_here
+GITHUB_MCP_PAT=your_token_here
 ```
 
 </details>
@@ -30,9 +30,18 @@ After securely storing your PAT, you can add the GitHub MCP server configuration
 
 > **Note:** For the most up-to-date configuration options, see the [main README.md](../../README.md).
 
-### Method 1: Remote Server (Recommended)
+### Method 1: Gemini Extension (Recommended)
 
-The simplest way is to use GitHub's hosted MCP server:
+The simplest way is to use GitHub's hosted MCP server via our gemini extension.
+
+`gemini extensions install https://github.com/github/github-mcp-server`
+
+> [!NOTE]
+> You will still need to have a personal access token with the appropriate scopes called `GITHUB_MCP_PAT` in your environment.
+
+### Method 2: Remote Server
+
+You can also connect to the hosted MCP server directly. After securely storing your PAT, configure Gemini CLI with:
 
 ```json
 // ~/.gemini/settings.json
@@ -41,14 +50,14 @@ The simplest way is to use GitHub's hosted MCP server:
         "github": {
             "httpUrl": "https://api.githubcopilot.com/mcp/",
             "headers": {
-                "Authorization": "Bearer $GITHUB_PAT"
+                "Authorization": "Bearer $GITHUB_MCP_PAT"
             }
         }
     }
 }
 ```
 
-### Method 2: Local Docker
+### Method 3: Local Docker
 
 With docker running, you can run the GitHub MCP server in a container:
 
@@ -67,14 +76,14 @@ With docker running, you can run the GitHub MCP server in a container:
                 "ghcr.io/github/github-mcp-server"
             ],
             "env": {
-                "GITHUB_PERSONAL_ACCESS_TOKEN": "$GITHUB_PAT"
+                "GITHUB_PERSONAL_ACCESS_TOKEN": "$GITHUB_MCP_PAT"
             }
         }
     }
 }
 ```
 
-### Method 3: Binary
+### Method 4: Binary
 
 You can download the latest binary release from the [GitHub releases page](https://github.com/github/github-mcp-server/releases) or build it from source by running `go build -o github-mcp-server ./cmd/github-mcp-server`.
 
@@ -88,7 +97,7 @@ Then, replacing `/path/to/binary` with the actual path to your binary, configure
             "command": "/path/to/binary",
             "args": ["stdio"],
             "env": {
-                "GITHUB_PERSONAL_ACCESS_TOKEN": "$GITHUB_PAT"
+                "GITHUB_PERSONAL_ACCESS_TOKEN": "$GITHUB_MCP_PAT"
             }
         }
     }

gemini-extension.json

@@ -0,0 +1,13 @@
+{
+	"name": "github",
+	"version": "1.0.0",
+	"mcpServers": {
+		"github": {
+			"description": "Connect AI assistants to GitHub - manage repos, issues, PRs, and workflows through natural language.",
+			"httpUrl": "https://api.githubcopilot.com/mcp/",
+			"headers": {
+				"Authorization": "Bearer $GITHUB_MCP_PAT"
+			}
+		}
+	}
+}

internal/ghmcp/server.go

@@ -106,15 +106,10 @@ func NewMCPServer(cfg MCPServerConfig) (*server.MCPServer, error) {
 		},
 	}
 
-	enabledToolsets := cfg.EnabledToolsets
-	if cfg.DynamicToolsets {
-		// filter "all" from the enabled toolsets
-		enabledToolsets = make([]string, 0, len(cfg.EnabledToolsets))
-		for _, toolset := range cfg.EnabledToolsets {
-			if toolset != "all" {
-				enabledToolsets = append(enabledToolsets, toolset)
-			}
-		}
+	enabledToolsets, invalidToolsets := cleanToolsets(cfg.EnabledToolsets, cfg.DynamicToolsets)
+
+	if len(invalidToolsets) > 0 {
+		fmt.Fprintf(os.Stderr, "Invalid toolsets ignored: %s\n", strings.Join(invalidToolsets, ", "))
 	}
 
 	// Generate instructions based on enabled toolsets
@@ -470,3 +465,57 @@ func (t *bearerAuthTransport) RoundTrip(req *http.Request) (*http.Response, erro
 	req.Header.Set("Authorization", "Bearer "+t.token)
 	return t.transport.RoundTrip(req)
 }
+
+// cleanToolsets cleans and handles special toolset keywords:
+// - Duplicates are removed from the result
+// - Removes whitespaces
+// - Validates toolset names and returns invalid ones separately
+// - "all": Returns ["all"] immediately, ignoring all other toolsets
+// - when dynamicToolsets is true, filters out "all" from the enabled toolsets
+// - "default": Replaces with the actual default toolset IDs from GetDefaultToolsetIDs()
+// Returns: (validToolsets, invalidToolsets)
+func cleanToolsets(enabledToolsets []string, dynamicToolsets bool) ([]string, []string) {
+	seen := make(map[string]bool)
+	result := make([]string, 0, len(enabledToolsets))
+	invalid := make([]string, 0)
+	validIDs := github.GetValidToolsetIDs()
+
+	// Add non-default toolsets, removing duplicates and trimming whitespace
+	for _, toolset := range enabledToolsets {
+		trimmed := strings.TrimSpace(toolset)
+		if trimmed == "" {
+			continue
+		}
+		if !seen[trimmed] {
+			seen[trimmed] = true
+			if trimmed != github.ToolsetMetadataDefault.ID && trimmed != github.ToolsetMetadataAll.ID {
+				// Validate the toolset name
+				if validIDs[trimmed] {
+					result = append(result, trimmed)
+				} else {
+					invalid = append(invalid, trimmed)
+				}
+			}
+		}
+	}
+
+	hasDefault := seen[github.ToolsetMetadataDefault.ID]
+	hasAll := seen[github.ToolsetMetadataAll.ID]
+
+	// Handle "all" keyword - return early if not in dynamic mode
+	if hasAll && !dynamicToolsets {
+		return []string{github.ToolsetMetadataAll.ID}, invalid
+	}
+
+	// Expand "default" keyword to actual default toolsets
+	if hasDefault {
+		for _, defaultToolset := range github.GetDefaultToolsetIDs() {
+			if !seen[defaultToolset] {
+				result = append(result, defaultToolset)
+				seen[defaultToolset] = true
+			}
+		}
+	}
+
+	return result, invalid
+}