Add --exclude-tools (and X-MCP-Exclude-Tools) flag to enable shutting off tools as part of server configuration

cmd/github-mcp-server/main.go

@@ -61,6 +61,14 @@ var (
 				}
 			}
 
+			// Parse excluded tools (similar to tools)
+			var excludeTools []string
+			if viper.IsSet("exclude_tools") {
+				if err := viper.UnmarshalKey("exclude_tools", &excludeTools); err != nil {
+					return fmt.Errorf("failed to unmarshal exclude-tools: %w", err)
+				}
+			}
+
 			// Parse enabled features (similar to toolsets)
 			var enabledFeatures []string
 			if viper.IsSet("features") {
@@ -85,6 +93,7 @@ var (
 				ContentWindowSize:    viper.GetInt("content-window-size"),
 				LockdownMode:         viper.GetBool("lockdown-mode"),
 				InsidersMode:         viper.GetBool("insiders"),
+				ExcludeTools:         excludeTools,
 				RepoAccessCacheTTL:   &ttl,
 			}
 			return ghmcp.RunStdioServer(stdioServerConfig)
@@ -126,6 +135,7 @@ func init() {
 	// Add global flags that will be shared by all commands
 	rootCmd.PersistentFlags().StringSlice("toolsets", nil, github.GenerateToolsetsHelp())
 	rootCmd.PersistentFlags().StringSlice("tools", nil, "Comma-separated list of specific tools to enable")
+	rootCmd.PersistentFlags().StringSlice("exclude-tools", nil, "Comma-separated list of tool names to disable regardless of other settings")
 	rootCmd.PersistentFlags().StringSlice("features", nil, "Comma-separated list of feature flags to enable")
 	rootCmd.PersistentFlags().Bool("dynamic-toolsets", false, "Enable dynamic toolsets")
 	rootCmd.PersistentFlags().Bool("read-only", false, "Restrict the server to read-only operations")
@@ -147,6 +157,7 @@ func init() {
 	// Bind flag to viper
 	_ = viper.BindPFlag("toolsets", rootCmd.PersistentFlags().Lookup("toolsets"))
 	_ = viper.BindPFlag("tools", rootCmd.PersistentFlags().Lookup("tools"))
+	_ = viper.BindPFlag("exclude_tools", rootCmd.PersistentFlags().Lookup("exclude-tools"))
 	_ = viper.BindPFlag("features", rootCmd.PersistentFlags().Lookup("features"))
 	_ = viper.BindPFlag("dynamic_toolsets", rootCmd.PersistentFlags().Lookup("dynamic-toolsets"))
 	_ = viper.BindPFlag("read-only", rootCmd.PersistentFlags().Lookup("read-only"))

docs/server-configuration.md

@@ -9,6 +9,7 @@ We currently support the following ways in which the GitHub MCP Server can be co
 |---------------|---------------|--------------|
 | Toolsets | `X-MCP-Toolsets` header or `/x/{toolset}` URL | `--toolsets` flag or `GITHUB_TOOLSETS` env var |
 | Individual Tools | `X-MCP-Tools` header | `--tools` flag or `GITHUB_TOOLS` env var |
+| Exclude Tools | `X-MCP-Exclude-Tools` header | `--exclude-tools` flag or `GITHUB_EXCLUDE_TOOLS` env var |
 | Read-Only Mode | `X-MCP-Readonly` header or `/readonly` URL | `--read-only` flag or `GITHUB_READ_ONLY` env var |
 | Dynamic Mode | Not available | `--dynamic-toolsets` flag or `GITHUB_DYNAMIC_TOOLSETS` env var |
 | Lockdown Mode | `X-MCP-Lockdown` header | `--lockdown-mode` flag or `GITHUB_LOCKDOWN_MODE` env var |
@@ -20,10 +21,12 @@ We currently support the following ways in which the GitHub MCP Server can be co
 
 ## How Configuration Works
 
-All configuration options are **composable**: you can combine toolsets, individual tools, dynamic discovery, read-only mode and lockdown mode in any way that suits your workflow.
+All configuration options are **composable**: you can combine toolsets, individual tools, excluded tools, dynamic discovery, read-only mode and lockdown mode in any way that suits your workflow.
 
 Note: **read-only** mode acts as a strict security filter that takes precedence over any other configuration, by disabling write tools even when explicitly requested.
 
+Note: **excluded tools** takes precedence over toolsets and individual tools — listed tools are always excluded, even if their toolset is enabled or they are explicitly added via `--tools` / `X-MCP-Tools`.
+
 ---
 
 ## Configuration Examples
@@ -170,6 +173,56 @@ Enable entire toolsets, then add individual tools from toolsets you don't want f
 
 ---
 
+### Excluding Specific Tools
+
+**Best for:** Users who want to enable a broad toolset but need to exclude specific tools for security, compliance, or to prevent undesired behavior.
+
+Listed tools are removed regardless of any other configuration — even if their toolset is enabled or they are individually added.
+
+<table>
+<tr><th>Remote Server</th><th>Local Server</th></tr>
+<tr valign="top">
+<td>
+
+```json
+{
+  "type": "http",
+  "url": "https://api.githubcopilot.com/mcp/",
+  "headers": {
+    "X-MCP-Toolsets": "pull_requests",
+    "X-MCP-Exclude-Tools": "create_pull_request,merge_pull_request"
+  }
+}
+```
+
+</td>
+<td>
+
+```json
+{
+  "type": "stdio",
+  "command": "go",
+  "args": [
+    "run",
+    "./cmd/github-mcp-server",
+    "stdio",
+    "--toolsets=pull_requests",
+    "--exclude-tools=create_pull_request,merge_pull_request"
+  ],
+  "env": {
+    "GITHUB_PERSONAL_ACCESS_TOKEN": "${input:github_token}"
+  }
+}
+```
+
+</td>
+</tr>
+</table>
+
+**Result:** All pull request tools except `create_pull_request` and `merge_pull_request` — the user gets read and review tools only.
+
+---
+
 ### Read-Only Mode
 
 **Best for:** Security conscious users who want to ensure the server won't allow operations that modify issues, pull requests, repositories etc.

internal/ghmcp/server.go

@@ -135,6 +135,7 @@ func NewStdioMCPServer(ctx context.Context, cfg github.MCPServerConfig) (*mcp.Se
 		WithReadOnly(cfg.ReadOnly).
 		WithToolsets(github.ResolvedEnabledToolsets(cfg.DynamicToolsets, cfg.EnabledToolsets, cfg.EnabledTools)).
 		WithTools(github.CleanTools(cfg.EnabledTools)).
+		WithExcludeTools(cfg.ExcludeTools).
 		WithServerInstructions().
 		WithFeatureChecker(featureChecker).
 		WithInsidersMode(cfg.InsidersMode)
@@ -214,6 +215,11 @@ type StdioServerConfig struct {
 	// InsidersMode indicates if we should enable experimental features
 	InsidersMode bool
 
+	// ExcludeTools is a list of tool names to disable regardless of other settings.
+	// These tools will be excluded even if their toolset is enabled or they are
+	// explicitly listed in EnabledTools.
+	ExcludeTools []string
+
 	// RepoAccessCacheTTL overrides the default TTL for repository access cache entries.
 	RepoAccessCacheTTL *time.Duration
 }
@@ -271,6 +277,7 @@ func RunStdioServer(cfg StdioServerConfig) error {
 		ContentWindowSize: cfg.ContentWindowSize,
 		LockdownMode:      cfg.LockdownMode,
 		InsidersMode:      cfg.InsidersMode,
+		ExcludeTools:      cfg.ExcludeTools,
 		Logger:            logger,
 		RepoAccessTTL:     cfg.RepoAccessCacheTTL,
 		TokenScopes:       tokenScopes,

pkg/context/request.go

@@ -82,6 +82,22 @@ func IsInsidersMode(ctx context.Context) bool {
 	return false
 }
 
+// excludeToolsCtxKey is a context key for excluded tools
+type excludeToolsCtxKey struct{}
+
+// WithExcludeTools adds the excluded tools to the context
+func WithExcludeTools(ctx context.Context, tools []string) context.Context {
+	return context.WithValue(ctx, excludeToolsCtxKey{}, tools)
+}
+
+// GetExcludeTools retrieves the excluded tools from the context
+func GetExcludeTools(ctx context.Context) []string {
+	if tools, ok := ctx.Value(excludeToolsCtxKey{}).([]string); ok {
+		return tools
+	}
+	return nil
+}
+
 // headerFeaturesCtxKey is a context key for raw header feature flags
 type headerFeaturesCtxKey struct{}
 

pkg/github/server.go

@@ -62,6 +62,11 @@ type MCPServerConfig struct {
 	// RepoAccessTTL overrides the default TTL for repository access cache entries.
 	RepoAccessTTL *time.Duration
 
+	// ExcludeTools is a list of tool names that should be disabled regardless of
+	// other configuration. These tools will be excluded even if their toolset is enabled
+	// or they are explicitly listed in EnabledTools.
+	ExcludeTools []string
+
 	// TokenScopes contains the OAuth scopes available to the token.
 	// When non-nil, tools requiring scopes not in this list will be hidden.
 	// This is used for PAT scope filtering where we can't issue scope challenges.

pkg/http/handler.go

@@ -275,6 +275,10 @@ func InventoryFiltersForRequest(r *http.Request, builder *inventory.Builder) *in
 		builder = builder.WithTools(github.CleanTools(tools))
 	}
 
+	if excluded := ghcontext.GetExcludeTools(ctx); len(excluded) > 0 {
+		builder = builder.WithExcludeTools(excluded)
+	}
+
 	return builder
 }
 

pkg/http/handler_test.go

@@ -104,6 +104,31 @@ func TestInventoryFiltersForRequest(t *testing.T) {
 			},
 			expectedTools: []string{"get_file_contents", "create_repository", "list_issues"},
 		},
+		{
+			name: "excluded tools removes specific tools",
+			contextSetup: func(ctx context.Context) context.Context {
+				return ghcontext.WithExcludeTools(ctx, []string{"create_repository", "issue_write"})
+			},
+			expectedTools: []string{"get_file_contents", "list_issues"},
+		},
+		{
+			name: "excluded tools overrides explicit tools",
+			contextSetup: func(ctx context.Context) context.Context {
+				ctx = ghcontext.WithTools(ctx, []string{"list_issues", "create_repository"})
+				ctx = ghcontext.WithExcludeTools(ctx, []string{"create_repository"})
+				return ctx
+			},
+			expectedTools: []string{"list_issues"},
+		},
+		{
+			name: "excluded tools combines with readonly",
+			contextSetup: func(ctx context.Context) context.Context {
+				ctx = ghcontext.WithReadonly(ctx, true)
+				ctx = ghcontext.WithExcludeTools(ctx, []string{"list_issues"})
+				return ctx
+			},
+			expectedTools: []string{"get_file_contents"},
+		},
 	}
 
 	for _, tt := range tests {
@@ -267,6 +292,40 @@ func TestHTTPHandlerRoutes(t *testing.T) {
 			},
 			expectedTools: []string{"get_file_contents", "create_repository", "list_issues", "create_issue", "list_pull_requests", "create_pull_request", "hidden_by_holdback"},
 		},
+		{
+			name: "X-MCP-Exclude-Tools header removes specific tools",
+			path: "/",
+			headers: map[string]string{
+				headers.MCPExcludeToolsHeader: "create_issue,create_pull_request",
+			},
+			expectedTools: []string{"get_file_contents", "create_repository", "list_issues", "list_pull_requests", "hidden_by_holdback"},
+		},
+		{
+			name: "X-MCP-Exclude-Tools with toolset header",
+			path: "/",
+			headers: map[string]string{
+				headers.MCPToolsetsHeader:     "issues",
+				headers.MCPExcludeToolsHeader: "create_issue",
+			},
+			expectedTools: []string{"list_issues"},
+		},
+		{
+			name: "X-MCP-Exclude-Tools overrides X-MCP-Tools",
+			path: "/",
+			headers: map[string]string{
+				headers.MCPToolsHeader:        "list_issues,create_issue",
+				headers.MCPExcludeToolsHeader: "create_issue",
+			},
+			expectedTools: []string{"list_issues"},
+		},
+		{
+			name: "X-MCP-Exclude-Tools with readonly path",
+			path: "/readonly",
+			headers: map[string]string{
+				headers.MCPExcludeToolsHeader: "list_issues",
+			},
+			expectedTools: []string{"get_file_contents", "list_pull_requests", "hidden_by_holdback"},
+		},
 	}
 
 	for _, tt := range tests {

pkg/http/headers/headers.go

@@ -41,6 +41,9 @@ const (
 	MCPLockdownHeader = "X-MCP-Lockdown"
 	// MCPInsidersHeader indicates whether insiders mode is enabled for early access features.
 	MCPInsidersHeader = "X-MCP-Insiders"
+	// MCPExcludeToolsHeader is a comma-separated list of MCP tools that should be
+	// disabled regardless of other settings or header values.
+	MCPExcludeToolsHeader = "X-MCP-Exclude-Tools"
 	// MCPFeaturesHeader is a comma-separated list of feature flags to enable.
 	MCPFeaturesHeader = "X-MCP-Features"
 

pkg/http/middleware/request_config.go

@@ -35,6 +35,11 @@ func WithRequestConfig(next http.Handler) http.Handler {
 			ctx = ghcontext.WithLockdownMode(ctx, true)
 		}
 
+		// Excluded tools
+		if excludeTools := headers.ParseCommaSeparated(r.Header.Get(headers.MCPExcludeToolsHeader)); len(excludeTools) > 0 {
+			ctx = ghcontext.WithExcludeTools(ctx, excludeTools)
+		}
+
 		// Insiders mode
 		if relaxedParseBool(r.Header.Get(headers.MCPInsidersHeader)) {
 			ctx = ghcontext.WithInsidersMode(ctx, true)

pkg/inventory/builder.go

@@ -141,6 +141,19 @@ func (b *Builder) WithFilter(filter ToolFilter) *Builder {
 	return b
 }
 
+// WithExcludeTools specifies tools that should be disabled regardless of other settings.
+// These tools will be excluded even if their toolset is enabled or they are in the
+// additional tools list. This takes precedence over all other tool enablement settings.
+// Input is cleaned (trimmed, deduplicated) before applying.
+// Returns self for chaining.
+func (b *Builder) WithExcludeTools(toolNames []string) *Builder {
+	cleaned := cleanTools(toolNames)
+	if len(cleaned) > 0 {
+		b.filters = append(b.filters, CreateExcludeToolsFilter(cleaned))
+	}
+	return b
+}
+
 // WithInsidersMode enables or disables insiders mode features.
 // When insiders mode is disabled (default), UI metadata is removed from tools
 // so clients won't attempt to load UI resources.
@@ -150,6 +163,20 @@ func (b *Builder) WithInsidersMode(enabled bool) *Builder {
 	return b
 }
 
+// CreateExcludeToolsFilter creates a ToolFilter that excludes tools by name.
+// Any tool whose name appears in the excluded list will be filtered out.
+// The input slice should already be cleaned (trimmed, deduplicated).
+func CreateExcludeToolsFilter(excluded []string) ToolFilter {
+	set := make(map[string]struct{}, len(excluded))
+	for _, name := range excluded {
+		set[name] = struct{}{}
+	}
+	return func(_ context.Context, tool *ServerTool) (bool, error) {
+		_, blocked := set[tool.Tool.Name]
+		return !blocked, nil
+	}
+}
+
 // cleanTools trims whitespace and removes duplicates from tool names.
 // Empty strings after trimming are excluded.
 func cleanTools(tools []string) []string {