[pull] main from github:main

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:
 
@@ -373,9 +370,25 @@ 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 (all are on by default):
+The following sets of tools are available:
 
 <!-- START AUTOMATED TOOLSETS -->
 | Toolset                 | Description                                                   |
@@ -400,6 +413,14 @@ The following sets of tools are available (all are on by default):
 | `users` | GitHub User related tools |
 <!-- END AUTOMATED TOOLSETS -->
 
+### Additional Toolsets in Remote Github MCP Server
+
+| Toolset                 | Description                                                   |
+| ----------------------- | ------------------------------------------------------------- |
+| `copilot` | Copilot related tools (e.g. Copilot Coding Agent) |
+| `copilot_spaces` | Copilot Spaces related tools |
+| `github_support_docs_search` | Search docs to answer GitHub product and support questions |
+
 ## Tools
 
 <!-- START AUTOMATED TOOLS -->
@@ -1167,7 +1188,7 @@ Possible options:
 
 <details>
 
-<summary>Copilot coding agent</summary>
+<summary>Copilot</summary>
 
 -   **create_pull_request_with_copilot** - Perform task with GitHub Copilot coding agent
     -   `owner`: Repository owner. You can guess the owner, but confirm it with the user before proceeding. (string, required)
@@ -1189,6 +1210,14 @@ Possible options:
 -   **list_copilot_spaces** - List Copilot Spaces
 </details>
 
+<details>
+
+<summary>GitHub Support Docs Search</summary>
+
+-   **github_support_docs_search** - Retrieve documentation relevant to answer GitHub product and support questions. Support topics include: GitHub Actions Workflows, Authentication, GitHub Support Inquiries, Pull Request Practices, Repository Maintenance, GitHub Pages, GitHub Packages, GitHub Discussions, Copilot Spaces
+    -   `query`: Input from the user about the question they need answered. This is the latest raw unedited user message. You should ALWAYS leave the user message as it is, you should never modify it. (string, required)
+</details>
+
 ## Dynamic Tool Discovery
 
 **Note**: This feature is currently in beta and may not be available in all environments. Please test it out and let us know if you encounter any issues.

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

@@ -40,7 +40,6 @@ The simplest way is to use GitHub's hosted MCP server:
     "mcpServers": {
         "github": {
             "httpUrl": "https://api.githubcopilot.com/mcp/",
-            "trust": true,
             "headers": {
                 "Authorization": "Bearer $GITHUB_PAT"
             }
@@ -122,6 +121,10 @@ To verify that the GitHub MCP server has been configured, start Gemini CLI in yo
     List my GitHub repositories
     ```
 
+## Additional Configuration
+
+You can find more MCP configuration options for Gemini CLI here: [MCP Configuration Structure](https://google-gemini.github.io/gemini-cli/docs/tools/mcp-server.html#configuration-structure). For example, bypassing tool confirmations or excluding specific tools.
+
 ## Troubleshooting
 
 ### Local Server Issues

docs/remote-server.md

@@ -46,7 +46,9 @@ These toolsets are only available in the remote GitHub MCP Server and are not in
 
 | Name                 | Description                                   | API URL                                     | 1-Click Install (VS Code)                                                                                                                                                                          | Read-only Link                                                    | 1-Click Read-only Install (VS Code)                                                                                                                                                                                     |
 | -------------------- | --------------------------------------------- | ------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ----------------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| Copilot coding agent | Perform task with GitHub Copilot coding agent | https://api.githubcopilot.com/mcp/x/copilot | [Install](https://insiders.vscode.dev/redirect/mcp/install?name=gh-copilot&config=%7B%22type%22%3A%20%22http%22%2C%22url%22%3A%20%22https%3A%2F%2Fapi.githubcopilot.com%2Fmcp%2Fx%2Fcopilot%22%7D) | [read-only](https://api.githubcopilot.com/mcp/x/copilot/readonly) | [Install read-only](https://insiders.vscode.dev/redirect/mcp/install?name=gh-copilot&config=%7B%22type%22%3A%20%22http%22%2C%22url%22%3A%20%22https%3A%2F%2Fapi.githubcopilot.com%2Fmcp%2Fx%2Fcopilot%2Freadonly%22%7D) |
+| Copilot  | Copilot related tools | https://api.githubcopilot.com/mcp/x/copilot | [Install](https://insiders.vscode.dev/redirect/mcp/install?name=gh-copilot&config=%7B%22type%22%3A%20%22http%22%2C%22url%22%3A%20%22https%3A%2F%2Fapi.githubcopilot.com%2Fmcp%2Fx%2Fcopilot%22%7D)             | [read-only](https://api.githubcopilot.com/mcp/x/copilot/readonly)                                        | [Install read-only](https://insiders.vscode.dev/redirect/mcp/install?name=gh-copilot&config=%7B%22type%22%3A%20%22http%22%2C%22url%22%3A%20%22https%3A%2F%2Fapi.githubcopilot.com%2Fmcp%2Fx%2Fcopilot%2Freadonly%22%7D)                                                              |
+| Copilot Spaces  | Copilot Spaces tools | https://api.githubcopilot.com/mcp/x/copilot_spaces    | [Install](https://insiders.vscode.dev/redirect/mcp/install?name=gh-copilot_spaces&config=%7B%22type%22%3A%20%22http%22%2C%22url%22%3A%20%22https%3A%2F%2Fapi.githubcopilot.com%2Fmcp%2Fx%2Fcopilot_spaces%22%7D)             | [read-only](https://api.githubcopilot.com/mcp/x/copilot_spaces/readonly)                                        | [Install read-only](https://insiders.vscode.dev/redirect/mcp/install?name=gh-copilot_spaces&config=%7B%22type%22%3A%20%22http%22%2C%22url%22%3A%20%22https%3A%2F%2Fapi.githubcopilot.com%2Fmcp%2Fx%2Fcopilot_spaces%2Freadonly%22%7D)                                                              |
+| GitHub support docs search | Retrieve documentation to answer GitHub product and support questions. Topics include: GitHub Actions Workflows, Authentication, ... | https://api.githubcopilot.com/mcp/x/github_support_docs_search | [Install](https://insiders.vscode.dev/redirect/mcp/install?name=gh-support&config=%7B%22type%22%3A%20%22http%22%2C%22url%22%3A%20%22https%3A%2F%2Fapi.githubcopilot.com%2Fmcp%2Fx%2Fgithub_support_docs_search%22%7D) | [read-only](https://api.githubcopilot.com/mcp/x/github_support_docs_search/readonly) | [Install read-only](https://insiders.vscode.dev/redirect/mcp/install?name=gh-support&config=%7B%22type%22%3A%20%22http%22%2C%22url%22%3A%20%22https%3A%2F%2Fapi.githubcopilot.com%2Fmcp%2Fx%2Fgithub_support_docs_search%2Freadonly%22%7D) |
 
 ### Optional Headers
 

internal/ghmcp/server.go

@@ -12,6 +12,7 @@ import (
 	"os/signal"
 	"strings"
 	"syscall"
+	"time"
 
 	"github.com/github/github-mcp-server/pkg/errors"
 	"github.com/github/github-mcp-server/pkg/github"
@@ -105,15 +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
@@ -363,11 +359,30 @@ func newGHESHost(hostname string) (apiHost, error) {
 		return apiHost{}, fmt.Errorf("failed to parse GHES GraphQL URL: %w", err)
 	}
 
-	uploadURL, err := url.Parse(fmt.Sprintf("%s://%s/api/uploads/", u.Scheme, u.Hostname()))
+	// Check if subdomain isolation is enabled
+	// See https://docs.github.com/en/enterprise-server@3.17/admin/configuring-settings/hardening-security-for-your-enterprise/enabling-subdomain-isolation#about-subdomain-isolation
+	hasSubdomainIsolation := checkSubdomainIsolation(u.Scheme, u.Hostname())
+
+	var uploadURL *url.URL
+	if hasSubdomainIsolation {
+		// With subdomain isolation: https://uploads.hostname/
+		uploadURL, err = url.Parse(fmt.Sprintf("%s://uploads.%s/", u.Scheme, u.Hostname()))
+	} else {
+		// Without subdomain isolation: https://hostname/api/uploads/
+		uploadURL, err = url.Parse(fmt.Sprintf("%s://%s/api/uploads/", u.Scheme, u.Hostname()))
+	}
 	if err != nil {
 		return apiHost{}, fmt.Errorf("failed to parse GHES Upload URL: %w", err)
 	}
-	rawURL, err := url.Parse(fmt.Sprintf("%s://%s/raw/", u.Scheme, u.Hostname()))
+
+	var rawURL *url.URL
+	if hasSubdomainIsolation {
+		// With subdomain isolation: https://raw.hostname/
+		rawURL, err = url.Parse(fmt.Sprintf("%s://raw.%s/", u.Scheme, u.Hostname()))
+	} else {
+		// Without subdomain isolation: https://hostname/raw/
+		rawURL, err = url.Parse(fmt.Sprintf("%s://%s/raw/", u.Scheme, u.Hostname()))
+	}
 	if err != nil {
 		return apiHost{}, fmt.Errorf("failed to parse GHES Raw URL: %w", err)
 	}
@@ -380,6 +395,29 @@ func newGHESHost(hostname string) (apiHost, error) {
 	}, nil
 }
 
+// checkSubdomainIsolation detects if GitHub Enterprise Server has subdomain isolation enabled
+// by attempting to ping the raw.<host>/_ping endpoint on the subdomain. The raw subdomain must always exist for subdomain isolation.
+func checkSubdomainIsolation(scheme, hostname string) bool {
+	subdomainURL := fmt.Sprintf("%s://raw.%s/_ping", scheme, hostname)
+
+	client := &http.Client{
+		Timeout: 5 * time.Second,
+		// Don't follow redirects - we just want to check if the endpoint exists
+		//nolint:revive // parameters are required by http.Client.CheckRedirect signature
+		CheckRedirect: func(req *http.Request, via []*http.Request) error {
+			return http.ErrUseLastResponse
+		},
+	}
+
+	resp, err := client.Get(subdomainURL)
+	if err != nil {
+		return false
+	}
+	defer resp.Body.Close()
+
+	return resp.StatusCode == http.StatusOK
+}
+
 // Note that this does not handle ports yet, so development environments are out.
 func parseAPIHost(s string) (apiHost, error) {
 	if s == "" {
@@ -427,3 +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
+}