chore: update readme for tool parititioning

README.md

@@ -110,6 +110,88 @@ If you don't have Docker, you can use `go build` to build the binary in the
 }
 ```
 
+## 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
@@ -331,7 +413,6 @@ 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)
@@ -341,50 +422,43 @@ 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)
@@ -405,16 +479,15 @@ 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)