refactor(tools): Modularize tool system with self-registering plugins

CLAUDE.md

@@ -28,8 +28,9 @@ The server uses a pluggable transport architecture:
 
 ### Tool and Security Framework
 - `mcp-server-tools.el` - Tool registry and execution framework
-- `mcp-server-emacs-tools.el` - Emacs-specific tool implementations
+- `mcp-server-emacs-tools.el` - Tool loader (loads tools from `tools/` directory)
 - `mcp-server-security.el` - Permission management and sandboxing
+- `tools/` - Individual tool implementations (self-registering modules)
 
 ## Essential Commands
 
@@ -87,10 +88,16 @@ The server supports multiple socket naming strategies via `mcp-server-socket-nam
 
 ## MCP Tool Registry
 
-The server exposes the following tool:
+The server exposes the following tools:
 
-### Elisp Execution
 - `eval-elisp` - Execute arbitrary Elisp expressions safely
+- `get-diagnostics` - Get flycheck/flymake diagnostics from project buffers
+
+Tools can be selectively enabled via `mcp-server-emacs-tools-enabled`:
+```elisp
+(setq mcp-server-emacs-tools-enabled 'all)              ; All tools (default)
+(setq mcp-server-emacs-tools-enabled '(get-diagnostics)) ; Only diagnostics
+```
 
 ## Security Model
 
@@ -150,19 +157,44 @@ if client.connect() and client.initialize():
 ## Development Workflow
 
 ### Adding New Tools
+
+Create a new file in `tools/` directory:
+
 ```elisp
-(mcp-server-tools-register
- "tool-name"
- "Display Title"
- "Description of functionality"
- '((type . "object")
-   (properties . ((param . ((type . "string")))))
-   (required . ["param"]))
- (lambda (args)
-   (let ((param (alist-get 'param args)))
-     (format "Result: %s" param))))
+;;; tools/mcp-server-emacs-tools-my-tool.el
+(require 'mcp-server-tools)
+
+(defun mcp-server-emacs-tools--my-tool-handler (args)
+  "Handle my-tool invocation with ARGS."
+  (let ((param (alist-get 'param args)))
+    (format "Result: %s" param)))
+
+(mcp-server-register-tool
+ (make-mcp-server-tool
+  :name "my-tool"
+  :title "My Tool"
+  :description "Description of functionality"
+  :input-schema '((type . "object")
+                  (properties . ((param . ((type . "string")))))
+                  (required . ["param"]))
+  :function #'mcp-server-emacs-tools--my-tool-handler))
+
+(provide 'mcp-server-emacs-tools-my-tool)
 ```
 
+Then register it in `mcp-server-emacs-tools.el`:
+
+```elisp
+;; Add to mcp-server-emacs-tools--available alist:
+(defconst mcp-server-emacs-tools--available
+  '((eval-elisp . mcp-server-emacs-tools-eval-elisp)
+    (get-diagnostics . mcp-server-emacs-tools-diagnostics)
+    (my-tool . mcp-server-emacs-tools-my-tool))  ; Add your tool here
+  "Alist mapping tool names (symbols) to their feature names.")
+```
+
+The tool will self-register when loaded. Use `mcp-server-emacs-tools-enabled` to control which tools are exposed to LLM clients.
+
 ### Testing Changes
 1. Run `./test/scripts/test-runner.sh` to validate core functionality
 2. Test with actual MCP clients using wrapper scripts
@@ -185,22 +217,20 @@ mcp-server/
 ├── mcp-server-transport-tcp.el      # TCP transport (planned)
 ├── mcp-server-tools.el              # Tool registry and execution
 ├── mcp-server-security.el           # Security and sandboxing
-├── mcp-server-emacs-tools.el        # Emacs-specific tool implementations
+├── mcp-server-emacs-tools.el        # Tool loader (loads from tools/)
+├── tools/                           # Individual tool implementations
+│   ├── mcp-server-emacs-tools-eval-elisp.el      # eval-elisp tool
+│   └── mcp-server-emacs-tools-diagnostics.el     # get-diagnostics tool
 ├── test/                            # Test suite directory
 │   ├── config/                      # Test configuration files
-│   │   ├── test-config.el           # Main test configuration
-│   │   ├── minimal-test-config.el   # Minimal test configuration
-│   │   └── test-json-false.el       # JSON serialization tests
+│   ├── fixtures/                    # Test helpers and utilities
+│   ├── unit/                        # Unit tests
+│   │   ├── test-mcp-emacs-tools.el  # Tool-specific tests
+│   │   └── ...
 │   ├── scripts/                     # Test runner scripts
-│   │   ├── test-runner.sh           # Comprehensive test suite
-│   │   ├── start-test-server.sh     # Test server startup
-│   │   ├── test-hello-world.sh      # Hello world test
-│   │   ├── test-hello-world.py      # Python test script
-│   │   └── debug-test.py            # Debug test utilities
+│   │   └── test-runner.sh           # Comprehensive test suite
 │   └── integration/                 # Integration test scripts
-│       ├── test-unix-socket-fixed.sh # Fixed Unix socket tests
-│       ├── test-unix-socket.sh      # Original socket tests
-├── mcp-wrapper.py                   # Python wrapper for MCP clients  
+├── mcp-wrapper.py                   # Python wrapper for MCP clients
 └── mcp-wrapper.sh                   # Shell wrapper for MCP clients
 ```
 

README.md

@@ -28,7 +28,7 @@ Alternatively, use package managers:
 ;; Using straight.el
 (use-package mcp-server
   :straight (:type git :host github :repo "rhblind/emacs-mcp-server"
-             :files ("*.el" "mcp-wrapper.py" "mcp-wrapper.sh"))
+             :files ("*.el" "tools/*.el" "mcp-wrapper.py" "mcp-wrapper.sh"))
   :config
   (add-hook 'emacs-startup-hook #'mcp-server-start-unix))
 
@@ -41,7 +41,7 @@ Alternatively, use package managers:
 ;; Using Doom Emacs package! macro
 (package! mcp-server
   :recipe (:type git :host github :repo "rhblind/emacs-mcp-server"
-           :files ("*.el" "mcp-wrapper.py" "mcp-wrapper.sh")))
+           :files ("*.el" "tools/*.el" "mcp-wrapper.py" "mcp-wrapper.sh")))
 ```
 
 **Start the server:** Run `M-x mcp-server-start-unix` in Emacs. The server creates a Unix socket at `~/.config/emacs/.local/cache/emacs-mcp-server.sock`. 
@@ -94,8 +94,41 @@ Once connected, LLMs can perform powerful operations in your Emacs environment:
 
 ## Available Tools
 
-**Current Tool:**
 - `eval-elisp` - Execute arbitrary elisp expressions safely and return the result
+- `get-diagnostics` - Get flycheck/flymake diagnostics from project buffers
+
+### get-diagnostics
+
+Retrieves errors and warnings from flycheck or flymake (auto-detected per buffer) across all project buffers. Results are grouped by file and sorted by severity.
+
+**Parameters:**
+| Parameter   | Type   | Required | Description                                   |
+|-------------|--------|----------|-----------------------------------------------|
+| `file_path` | string | No       | Get diagnostics for a specific file only      |
+| `severity`  | string | No       | Filter by `"error"`, `"warning"`, or `"info"` |
+
+**Example response:**
+```json
+{
+  "summary": {"total": 5, "errors": 2, "warnings": 3, "info": 0},
+  "files": {
+    "/path/to/file.el": {
+      "error_count": 2,
+      "warning_count": 1,
+      "info_count": 0,
+      "diagnostics": [
+        {
+          "line": 42,
+          "column": 10,
+          "message": "Unused variable 'foo'",
+          "severity": "warning",
+          "source": "emacs-lisp"
+        }
+      ]
+    }
+  }
+}
+```
 
 ## Configuration
 
@@ -108,6 +141,19 @@ Once connected, LLMs can perform powerful operations in your Emacs environment:
 (setq mcp-server-socket-name "custom")  ; Custom: emacs-mcp-server-custom.sock
 ```
 
+**Tool selection:** Choose which tools to enable:
+
+```elisp
+;; Enable all tools (default)
+(setq mcp-server-emacs-tools-enabled 'all)
+
+;; Enable only specific tools (disable eval-elisp for security)
+(setq mcp-server-emacs-tools-enabled '(get-diagnostics))
+
+;; Enable only eval-elisp
+(setq mcp-server-emacs-tools-enabled '(eval-elisp))
+```
+
 **Other configuration options:**
 
 ```elisp
@@ -123,7 +169,10 @@ Once connected, LLMs can perform powerful operations in your Emacs environment:
 
 ## Security
 
-The MCP server implements comprehensive security measures to protect your Emacs environment and sensitive data from unauthorized access by LLMs.
+> [!WARNING]
+> The MCP server implements certain security measures to protect your Emacs environment and sensitive data from unauthorized access by LLMs.
+> However, the `eval-elisp` tool enables arbitrary evaluation of Elisp code in your Emacs process and therefore by definition enables remote code execution for the LLM.
+> **Use this tool with extreme caution!**
 
 ### Security Features
 
@@ -368,19 +417,46 @@ print(response)
 **Quick test:** Run `./test/scripts/test-runner.sh` or test a specific socket with `./test/integration/test-unix-socket-fixed.sh ~/.emacs.d/.local/cache/emacs-mcp-server.sock`
 
 **Adding custom tools:**
+
+Create a new file in the `tools/` directory:
+
 ```elisp
-(mcp-server-tools-register
- "my-tool"
- "My Custom Tool"  
- "Description of what this tool does"
- '((type . "object")
-   (properties . ((param . ((type . "string")))))
-   (required . ["param"]))
- (lambda (args)
-   (let ((param (alist-get 'param args)))
-     (format "Result: %s" param))))
+;;; tools/mcp-server-emacs-tools-my-tool.el
+
+(require 'mcp-server-tools)
+
+(defun mcp-server-emacs-tools--my-tool-handler (args)
+  "Handle my-tool invocation with ARGS."
+  (let ((param (alist-get 'param args)))
+    (format "Result: %s" param)))
+
+(mcp-server-register-tool
+ (make-mcp-server-tool
+  :name "my-tool"
+  :title "My Custom Tool"
+  :description "Description of what this tool does"
+  :input-schema '((type . "object")
+                  (properties . ((param . ((type . "string")
+                                           (description . "A parameter")))))
+                  (required . ["param"]))
+  :function #'mcp-server-emacs-tools--my-tool-handler))
+
+(provide 'mcp-server-emacs-tools-my-tool)
 ```
 
+Then register it in `mcp-server-emacs-tools.el`:
+
+```elisp
+;; Add to mcp-server-emacs-tools--available alist:
+(defconst mcp-server-emacs-tools--available
+  '((eval-elisp . mcp-server-emacs-tools-eval-elisp)
+    (get-diagnostics . mcp-server-emacs-tools-diagnostics)
+    (my-tool . mcp-server-emacs-tools-my-tool))  ; Add your tool here
+  "Alist mapping tool names (symbols) to their feature names.")
+```
+
+The tool will self-register when loaded. Use `mcp-server-emacs-tools-enabled` to control which tools are exposed to LLM clients.
+
 ## Troubleshooting
 
 **Server won't start:**

mcp-server-emacs-tools.el

@@ -4,33 +4,62 @@
 
 ;;; Commentary:
 
-;; This module provides Emacs-specific MCP tools.
+;; This module loads Emacs-specific MCP tools from the tools/ directory.
+;; Tools self-register on require.  Use `mcp-server-emacs-tools-enabled'
+;; to control which tools are exposed to LLM clients at runtime.
 
 ;;; Code:
 
 (require 'mcp-server-tools)
-(require 'mcp-server-security)
-(require 'cl-lib)
-
-(defun mcp-server-emacs-tools-register ()
-  "Register all Emacs-specific MCP tools."
-
-  ;; eval-elisp - Execute arbitrary elisp expressions
-  (mcp-server-tools-register
-   "eval-elisp"
-   "Execute Elisp Expression"
-   "Execute arbitrary Elisp code and return the result."
-   '((type . "object")
-     (properties . ((expression . ((type . "string")
-                                   (description . "The Elisp expression to evaluate")))))
-     (required . ("expression")))
-   (lambda (args)
-     (let ((expression (alist-get 'expression args)))
-       (condition-case err
-           (let ((form (read-from-string expression)))
-             (format "%S" (mcp-server-security-safe-eval (car form))))
-         (error (format "Error: %s" (error-message-string err))))))))
+
+(defgroup mcp-server-emacs-tools nil
+  "Emacs-specific MCP tools configuration."
+  :group 'mcp-server
+  :prefix "mcp-server-emacs-tools-")
+
+(defcustom mcp-server-emacs-tools-enabled 'all
+  "Which MCP tools to enable.
+Can be `all' to enable all available tools, or a list of tool
+names (symbols) to enable selectively.
+
+Available tools:
+- `eval-elisp' - Execute arbitrary Elisp expressions
+- `get-diagnostics' - Get flycheck/flymake diagnostics
+
+Example: \\='(get-diagnostics) to enable only diagnostics.
+
+Changes take effect immediately - disabled tools are hidden from
+LLM clients and cannot be called."
+  :type '(choice (const :tag "All tools" all)
+                 (repeat :tag "Selected tools" symbol))
+  :group 'mcp-server-emacs-tools)
+
+(defconst mcp-server-emacs-tools--available
+  '((eval-elisp . mcp-server-emacs-tools-eval-elisp)
+    (get-diagnostics . mcp-server-emacs-tools-diagnostics))
+  "Alist mapping tool names (symbols) to their feature names.")
+
+;; Add tools directory to load path
+(let* ((this-file (or load-file-name buffer-file-name))
+       (tools-dir (and this-file
+                       (expand-file-name "tools" (file-name-directory this-file)))))
+  (when tools-dir
+    (add-to-list 'load-path tools-dir)))
+
+(defun mcp-server-emacs-tools--tool-enabled-p (tool-name)
+  "Return non-nil if TOOL-NAME is enabled.
+TOOL-NAME can be a string or symbol."
+  (let ((name-sym (if (stringp tool-name) (intern tool-name) tool-name)))
+    (or (eq mcp-server-emacs-tools-enabled 'all)
+        (memq name-sym mcp-server-emacs-tools-enabled))))
+
+;; Set up the filter for mcp-server-tools
+(setq mcp-server-tools-filter #'mcp-server-emacs-tools--tool-enabled-p)
+
+;; Load all tool modules (they self-register)
+(dolist (tool-spec mcp-server-emacs-tools--available)
+  (require (cdr tool-spec)))
 
 (provide 'mcp-server-emacs-tools)
 
-;;; mcp-server-emacs-tools.el ends here
+;;; mcp-server-emacs-tools.el ends here