Merge branch 'main' into notifications-tooling

Author: sridharavinash

.github/CODEOWNERS

@@ -1 +1 @@
-* @juruen @sammorrowdrums @williammartin @toby
+* @github/github-mcp-server

.gitignore

@@ -1,5 +1,12 @@
 .idea
 cmd/github-mcp-server/github-mcp-server
+
+# VSCode
+.vscode/mcp.json
+
 # Added by goreleaser init:
 dist/
-__debug_bin*
+__debug_bin*
+
+# Go 
+vendor

README.md

@@ -19,13 +19,11 @@ automation and interaction capabilities for developers and tools.
 3. Lastly you will need to [Create a GitHub Personal Access Token](https://github.com/settings/personal-access-tokens/new).
 The MCP server can use many of the GitHub APIs, so enable the permissions that you feel comfortable granting your AI tools (to learn more about access tokens, please check out the [documentation](https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/managing-your-personal-access-tokens)).
 
-
-
 ## Installation
 
 ### Usage with VS Code
 
-For quick installation, use one of the one-click install buttons at the top of this README.
+For quick installation, use one of the one-click install buttons at the top of this README. Once you complete that flow, toggle Agent mode (located by the Copilot Chat text input) and the server will start.
 
 For manual installation, add the following JSON block to your User Settings (JSON) file in VS Code. You can do this by pressing `Ctrl + Shift + P` and typing `Preferences: Open User Settings (JSON)`.
 
@@ -91,14 +89,110 @@ More about using MCP server tools in VS Code's [agent mode documentation](https:
 
 ### Build from source
 
-If you don't have Docker, you can use `go` to build the binary in the
-`cmd/github-mcp-server` directory, and use the `github-mcp-server stdio`
-command with the `GITHUB_PERSONAL_ACCESS_TOKEN` environment variable set to
-your token.
+If you don't have Docker, you can use `go build` to build the binary in the
+`cmd/github-mcp-server` directory, and use the `github-mcp-server stdio` command with the `GITHUB_PERSONAL_ACCESS_TOKEN` environment variable set to your token. To specify the output location of the build, use the `-o` flag. You should configure your server to use the built executable as its `command`. For example:
+
+```JSON
+{
+  "mcp": {
+    "servers": {
+      "github": {
+        "command": "/path/to/github-mcp-server",
+        "args": ["stdio"],
+        "env": {
+          "GITHUB_PERSONAL_ACCESS_TOKEN": "<YOUR_TOKEN>"
+        }
+      }
+    }
+  }
+}
+```
+
+## Tool Configuration
+
+The GitHub MCP Server supports enabling or disabling specific groups of functionalities via the `--toolsets` flag. This allows you to control which GitHub API capabilities are available to your AI tools. Enabling only the toolsets that you need can help the LLM with tool choice and reduce the context size.
+
+### Available Toolsets
+
+The following sets of tools are available (all are on by default):
+
+| Toolset                 | Description                                                   |
+| ----------------------- | ------------------------------------------------------------- |
+| `repos`                 | Repository-related tools (file operations, branches, commits) |
+| `issues`                | Issue-related tools (create, read, update, comment)           |
+| `users`                 | Anything relating to GitHub Users                             |
+| `pull_requests`         | Pull request operations (create, merge, review)               |
+| `code_security`         | Code scanning alerts and security features                    |
+| `experiments`           | Experimental features (not considered stable)                 |
+
+#### Specifying Toolsets
+
+To specify toolsets you want available to the LLM, you can pass an allow-list in two ways:
+
+1. **Using Command Line Argument**:
+
+   ```bash
+   github-mcp-server --toolsets repos,issues,pull_requests,code_security
+   ```
+
+2. **Using Environment Variable**:
+   ```bash
+   GITHUB_TOOLSETS="repos,issues,pull_requests,code_security" ./github-mcp-server
+   ```
+
+The environment variable `GITHUB_TOOLSETS` takes precedence over the command line argument if both are provided.
+
+### Using Toolsets With Docker
+
+When using Docker, you can pass the toolsets as environment variables:
+
+```bash
+docker run -i --rm \
+  -e GITHUB_PERSONAL_ACCESS_TOKEN=<your-token> \
+  -e GITHUB_TOOLSETS="repos,issues,pull_requests,code_security,experiments" \
+  ghcr.io/github/github-mcp-server
+```
+
+### The "all" Toolset
+
+The special toolset `all` can be provided to enable all available toolsets regardless of any other configuration:
+
+```bash
+./github-mcp-server --toolsets all
+```
+
+Or using the environment variable:
+
+```bash
+GITHUB_TOOLSETS="all" ./github-mcp-server
+```
+
+## 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.
+
+Instead of starting with all tools enabled, you can turn on dynamic toolset discovery. Dynamic toolsets allow the MCP host to list and enable toolsets in response to a user prompt. This should help to avoid situations where the model gets confused by the shear number of tools available.
+
+### Using Dynamic Tool Discovery
+
+When using the binary, you can pass the `--dynamic-toolsets` flag.
+
+```bash
+./github-mcp-server --dynamic-toolsets
+```
+
+When using Docker, you can pass the toolsets as environment variables:
+
+```bash
+docker run -i --rm \
+  -e GITHUB_PERSONAL_ACCESS_TOKEN=<your-token> \
+  -e GITHUB_DYNAMIC_TOOLSETS=1 \
+  ghcr.io/github/github-mcp-server
+```
 
 ## GitHub Enterprise Server
 
-The flag `--gh-host` and the environment variable `GH_HOST` can be used to set
+The flag `--gh-host` and the environment variable `GITHUB_HOST` can be used to set
 the GitHub Enterprise Server hostname.
 
 ## i18n / Overriding Descriptions
@@ -317,7 +411,6 @@ export GITHUB_MCP_TOOL_ADD_ISSUE_COMMENT_DESCRIPTION="an alternative description
 ### Repositories
 
 - **create_or_update_file** - Create or update a single file in a repository
-
   - `owner`: Repository owner (string, required)
   - `repo`: Repository name (string, required)
   - `path`: File path (string, required)
@@ -327,50 +420,43 @@ export GITHUB_MCP_TOOL_ADD_ISSUE_COMMENT_DESCRIPTION="an alternative description
   - `sha`: File SHA if updating (string, optional)
 
 - **list_branches** - List branches in a GitHub repository
-
   - `owner`: Repository owner (string, required)
   - `repo`: Repository name (string, required)
   - `page`: Page number (number, optional)
   - `perPage`: Results per page (number, optional)
 
 - **push_files** - Push multiple files in a single commit
-
   - `owner`: Repository owner (string, required)
   - `repo`: Repository name (string, required)
   - `branch`: Branch to push to (string, required)
   - `files`: Files to push, each with path and content (array, required)
   - `message`: Commit message (string, required)
 
 - **search_repositories** - Search for GitHub repositories
-
   - `query`: Search query (string, required)
   - `sort`: Sort field (string, optional)
   - `order`: Sort order (string, optional)
   - `page`: Page number (number, optional)
   - `perPage`: Results per page (number, optional)
 
 - **create_repository** - Create a new GitHub repository
-
   - `name`: Repository name (string, required)
   - `description`: Repository description (string, optional)
   - `private`: Whether the repository is private (boolean, optional)
   - `autoInit`: Auto-initialize with README (boolean, optional)
 
 - **get_file_contents** - Get contents of a file or directory
-
   - `owner`: Repository owner (string, required)
   - `repo`: Repository name (string, required)
   - `path`: File path (string, required)
   - `ref`: Git reference (string, optional)
 
 - **fork_repository** - Fork a repository
-
   - `owner`: Repository owner (string, required)
   - `repo`: Repository name (string, required)
   - `organization`: Target organization name (string, optional)
 
 - **create_branch** - Create a new branch
-
   - `owner`: Repository owner (string, required)
   - `repo`: Repository name (string, required)
   - `branch`: New branch name (string, required)
@@ -391,16 +477,15 @@ export GITHUB_MCP_TOOL_ADD_ISSUE_COMMENT_DESCRIPTION="an alternative description
   - `page`: Page number, for files in the commit (number, optional)
   - `perPage`: Results per page, for files in the commit (number, optional)
 
-### Search
-
-- **search_code** - Search for code across GitHub repositories
-
+  - **search_code** - Search for code across GitHub repositories
   - `query`: Search query (string, required)
   - `sort`: Sort field (string, optional)
   - `order`: Sort order (string, optional)
   - `page`: Page number (number, optional)
   - `perPage`: Results per page (number, optional)
 
+### Users
+
 - **search_users** - Search for GitHub users
   - `query`: Search query (string, required)
   - `sort`: Sort field (string, optional)
@@ -422,6 +507,22 @@ export GITHUB_MCP_TOOL_ADD_ISSUE_COMMENT_DESCRIPTION="an alternative description
   - `ref`: Git reference (string, optional)
   - `state`: Alert state (string, optional)
   - `severity`: Alert severity (string, optional)
+  - `tool_name`: The name of the tool used for code scanning (string, optional)
+
+### Secret Scanning
+
+- **get_secret_scanning_alert** - Get a secret scanning alert
+
+  - `owner`: Repository owner (string, required)
+  - `repo`: Repository name (string, required)
+  - `alertNumber`: Alert number (number, required)
+
+- **list_secret_scanning_alerts** - List secret scanning alerts for a repository
+  - `owner`: Repository owner (string, required)
+  - `repo`: Repository name (string, required)
+  - `state`: Alert state (string, optional)
+  - `secret_type`: The secret types to be filtered for in a comma-separated list (string, optional)
+  - `resolution`: The resolution status (string, optional)
 
 ## Resources
 

cmd/github-mcp-server/main.go

@@ -29,7 +29,7 @@ var (
 		Use:     "server",
 		Short:   "GitHub MCP Server",
 		Long:    `A GitHub MCP server that handles various tools and resources.`,
-		Version: fmt.Sprintf("%s (%s) %s", version, commit, date),
+		Version: fmt.Sprintf("Version: %s\nCommit: %s\nBuild Date: %s", version, commit, date),
 	}
 
 	stdioCmd = &cobra.Command{
@@ -44,12 +44,16 @@ var (
 			if err != nil {
 				stdlog.Fatal("Failed to initialize logger:", err)
 			}
+
+			enabledToolsets := viper.GetStringSlice("toolsets")
+
 			logCommands := viper.GetBool("enable-command-logging")
 			cfg := runConfig{
 				readOnly:           readOnly,
 				logger:             logger,
 				logCommands:        logCommands,
 				exportTranslations: exportTranslations,
+				enabledToolsets:    enabledToolsets,
 			}
 			if err := runStdioServer(cfg); err != nil {
 				stdlog.Fatal("failed to run stdio server:", err)
@@ -61,27 +65,33 @@ var (
 func init() {
 	cobra.OnInitialize(initConfig)
 
+	rootCmd.SetVersionTemplate("{{.Short}}\n{{.Version}}\n")
+
 	// Add global flags that will be shared by all commands
+	rootCmd.PersistentFlags().StringSlice("toolsets", github.DefaultTools, "An optional comma separated list of groups of tools to allow, defaults to enabling all")
+	rootCmd.PersistentFlags().Bool("dynamic-toolsets", false, "Enable dynamic toolsets")
 	rootCmd.PersistentFlags().Bool("read-only", false, "Restrict the server to read-only operations")
 	rootCmd.PersistentFlags().String("log-file", "", "Path to log file")
 	rootCmd.PersistentFlags().Bool("enable-command-logging", false, "When enabled, the server will log all command requests and responses to the log file")
 	rootCmd.PersistentFlags().Bool("export-translations", false, "Save translations to a JSON file")
 	rootCmd.PersistentFlags().String("gh-host", "", "Specify the GitHub hostname (for GitHub Enterprise etc.)")
 
 	// Bind flag to viper
+	_ = viper.BindPFlag("toolsets", rootCmd.PersistentFlags().Lookup("toolsets"))
+	_ = viper.BindPFlag("dynamic_toolsets", rootCmd.PersistentFlags().Lookup("dynamic-toolsets"))
 	_ = viper.BindPFlag("read-only", rootCmd.PersistentFlags().Lookup("read-only"))
 	_ = viper.BindPFlag("log-file", rootCmd.PersistentFlags().Lookup("log-file"))
 	_ = viper.BindPFlag("enable-command-logging", rootCmd.PersistentFlags().Lookup("enable-command-logging"))
 	_ = viper.BindPFlag("export-translations", rootCmd.PersistentFlags().Lookup("export-translations"))
-	_ = viper.BindPFlag("gh-host", rootCmd.PersistentFlags().Lookup("gh-host"))
+	_ = viper.BindPFlag("host", rootCmd.PersistentFlags().Lookup("gh-host"))
 
 	// Add subcommands
 	rootCmd.AddCommand(stdioCmd)
 }
 
 func initConfig() {
 	// Initialize Viper configuration
-	viper.SetEnvPrefix("APP")
+	viper.SetEnvPrefix("github")
 	viper.AutomaticEnv()
 }
 
@@ -107,6 +117,7 @@ type runConfig struct {
 	logger             *log.Logger
 	logCommands        bool
 	exportTranslations bool
+	enabledToolsets    []string
 }
 
 func runStdioServer(cfg runConfig) error {
@@ -115,18 +126,14 @@ func runStdioServer(cfg runConfig) error {
 	defer stop()
 
 	// Create GH client
-	token := os.Getenv("GITHUB_PERSONAL_ACCESS_TOKEN")
+	token := viper.GetString("personal_access_token")
 	if token == "" {
 		cfg.logger.Fatal("GITHUB_PERSONAL_ACCESS_TOKEN not set")
 	}
 	ghClient := gogithub.NewClient(nil).WithAuthToken(token)
 	ghClient.UserAgent = fmt.Sprintf("github-mcp-server/%s", version)
 
-	// Check GH_HOST env var first, then fall back to viper config
-	host := os.Getenv("GH_HOST")
-	if host == "" {
-		host = viper.GetString("gh-host")
-	}
+	host := viper.GetString("host")
 
 	if host != "" {
 		var err error
@@ -149,8 +156,40 @@ func runStdioServer(cfg runConfig) error {
 	hooks := &server.Hooks{
 		OnBeforeInitialize: []server.OnBeforeInitializeFunc{beforeInit},
 	}
-	// Create
-	ghServer := github.NewServer(getClient, version, cfg.readOnly, t, server.WithHooks(hooks))
+	// Create server
+	ghServer := github.NewServer(version, server.WithHooks(hooks))
+
+	enabled := cfg.enabledToolsets
+	dynamic := viper.GetBool("dynamic_toolsets")
+	if dynamic {
+		// filter "all" from the enabled toolsets
+		enabled = make([]string, 0, len(cfg.enabledToolsets))
+		for _, toolset := range cfg.enabledToolsets {
+			if toolset != "all" {
+				enabled = append(enabled, toolset)
+			}
+		}
+	}
+
+	// Create default toolsets
+	toolsets, err := github.InitToolsets(enabled, cfg.readOnly, getClient, t)
+	context := github.InitContextToolset(getClient, t)
+
+	if err != nil {
+		stdlog.Fatal("Failed to initialize toolsets:", err)
+	}
+
+	// Register resources with the server
+	github.RegisterResources(ghServer, getClient, t)
+	// Register the tools with the server
+	toolsets.RegisterTools(ghServer)
+	context.RegisterTools(ghServer)
+
+	if dynamic {
+		dynamic := github.InitDynamicToolset(ghServer, toolsets, t)
+		dynamic.RegisterTools(ghServer)
+	}
+
 	stdioServer := server.NewStdioServer(ghServer)
 
 	stdLogger := stdlog.New(cfg.logger.Writer(), "stdioserver", 0)

go.mod

@@ -6,7 +6,7 @@ require (
 	github.com/docker/docker v28.0.4+incompatible
 	github.com/google/go-cmp v0.7.0
 	github.com/google/go-github/v69 v69.2.0
-	github.com/mark3labs/mcp-go v0.18.0
+	github.com/mark3labs/mcp-go v0.20.1
 	github.com/migueleliasweb/go-github-mock v1.1.0
 	github.com/sirupsen/logrus v1.9.3
 	github.com/spf13/cobra v1.9.1