Added Advanced tab in Options with MCP integration toggle

CHANGELOG.md

@@ -1,3 +1,4 @@
+- Added Advanced tab in Tools → Options → Claude Code with Debug mode, Hang timeout, and a new "Enable MCP integration" toggle (disabling it skips the --mcp-config flag while hooks remain active)
 - Fixed process start errors and hang timeouts now logged to the IDE log file at SEVERE level
 - Added hang detection: configurable timeout (default 60 s) kills the process and shows an error if no PTY output is received after launch; set to 0 to disable
 - Fixed authentication for profiles with the "Claude API" connection type: the API key is now correctly recognised by Claude Code on session start

docs/user-manual.md

@@ -333,6 +333,8 @@ Open **Tools → Options → Claude Code** in NetBeans.
 
 ### General tab
 
+![Settings — General tab](screenshots/settings-general.png)
+
 | Setting | Default | Description |
 |---------|---------|-------------|
 | Claude CLI path | (empty) | Absolute path to the `claude` executable. Leave empty to use the system `PATH`. |
@@ -341,14 +343,25 @@ Open **Tools → Options → Claude Code** in NetBeans.
 | History TTL (days) | 0 | Number of days after which history entries expire. 0 = keep forever. |
 | Send prompt key | Ctrl+Enter | Key combination that sends the prompt from the input area. |
 | Insert newline key | Enter | Key combination that inserts a newline in the input area. The send and newline keys are configured independently but cannot be set to the same value. |
-| Debug mode | Off | Enables verbose logging of all Claude I/O to the NetBeans log file and the Output window. |
 | Open diff in a separate tab | Off | Opens the diff panel in a new IDE tab instead of embedding it in the session tab. |
 | Show markdown preview for .md files in diff | On | Shows a rendered markdown preview alongside the raw diff for `.md` files. |
 | Start new session when opening with Claude | Off (Continue last) | Checked → always start a **New session** when opening with the project context menu or when NetBeans restores a closed session tab on restart. Unchecked → **Continue last**. |
 | Session list limit | 30 | Maximum number of past sessions shown in the session selector table. |
 
+### Advanced tab
+
+![Settings — Advanced tab](screenshots/settings-advanced.png)
+
+| Setting | Default | Description |
+|---------|---------|-------------|
+| Debug mode | Off | Enables verbose logging of all Claude I/O to the NetBeans log file and the Output window. |
+| Hang timeout (seconds) | 60 | Kill the process if no PTY output is received within this many seconds after launch. Set to 0 to disable. |
+| Enable MCP integration | On | When unchecked, the `--mcp-config` flag is not passed to `claude`. Hooks (PreToolUse) are always configured regardless of this setting. Disable only if MCP causes issues. |
+
 ### Favorites tab
 
+![Settings — Favorites tab](screenshots/settings-favorites.png)
+
 Manages global favorites — prompts available in every project.
 
 The table shows all global favorites with columns: ☐ (checkbox for multi-select), **Text**, **Shortcut**.
@@ -365,6 +378,10 @@ The table shows all global favorites with columns: ☐ (checkbox for multi-selec
 
 The search field filters entries by text.
 
+### Profiles tab
+
+See [Section 12 — Profiles](#12-profiles) for full details on creating and managing profiles.
+
 ---
 
 ## 12. Profiles
@@ -651,14 +668,14 @@ As you move the cursor or change the selection in any open editor, the plugin au
 If Claude says a tool is unavailable (e.g. "I don't have access to `getWorkspaceFolders`"):
 
 1. Check that no other application is using the MCP server port (**Tools → Options → Claude Code → General → MCP server port**, default: 28991). Change the port if needed and restart the IDE.
-2. Enable **Debug mode** and check the log file (`~/.netbeans/<version>/var/log/messages.log`) for `MCP SSE server started on port`.
+2. Enable **Debug mode** (**Tools → Options → Claude Code → Advanced**) and check the log file (`~/.netbeans/<version>/var/log/messages.log`) for `MCP SSE server started on port`.
 
 ---
 
 ## 15. Troubleshooting
 
 ### Enable debug mode
-Go to **Tools → Options → Claude Code → General** and check **Debug mode**. This writes detailed logs of all Claude I/O (PTY bytes, MCP messages, hook calls) to the NetBeans log file.
+Go to **Tools → Options → Claude Code → Advanced** and check **Debug mode**. This writes detailed logs of all Claude I/O (PTY bytes, MCP messages, hook calls) to the NetBeans log file.
 
 ### Log file location
 ```

pom.xml

@@ -6,7 +6,7 @@
 
     <groupId>io.github.nbclaudecodegui</groupId>
     <artifactId>netbeans-claude-code-gui</artifactId>
-    <version>0.21.34-SNAPSHOT</version>
+    <version>0.21.36-SNAPSHOT</version>
     <packaging>nbm</packaging>
     <name>Netbeans Claude Code GUI</name>
     <description>NetBeans plugin that provides a GUI for Claude Code CLI — run claude code sessions directly inside the IDE.</description>

src/main/java/io/github/nbclaudecodegui/process/ClaudeProcess.java

@@ -163,11 +163,15 @@ public PtyProcess start(String workingDir, ClaudeProfile profile, String extraCl
                 + ", port=" + (mcp != null ? mcp.getServerPort() : -1));
         if (mcp != null && mcp.isServerRunning()) {
             int port = mcp.getServerPort();
-            // Pass MCP server config via --mcp-config (Claude 2.x no longer reads
-            // mcpServers from settings.local.json; --mcp-config works in TUI mode).
-            cmd.add("--mcp-config");
-            cmd.add(buildMcpConfigJson(port));
-            LOG.info("Passing --mcp-config with netbeans SSE server on port " + port);
+            if (io.github.nbclaudecodegui.settings.ClaudeCodePreferences.isMcpEnabled()) {
+                // Pass MCP server config via --mcp-config (Claude 2.x no longer reads
+                // mcpServers from settings.local.json; --mcp-config works in TUI mode).
+                cmd.add("--mcp-config");
+                cmd.add(buildMcpConfigJson(port));
+                LOG.info("Passing --mcp-config with netbeans SSE server on port " + port);
+            } else {
+                LOG.info("MCP integration disabled by user preference; skipping --mcp-config");
+            }
             try {
                 writeSettingsLocalJson(workingDir, port, profile);
             } catch (IOException e) {

src/main/java/io/github/nbclaudecodegui/settings/ClaudeCodeOptionsPanel.java

@@ -70,6 +70,8 @@ public final class ClaudeCodeOptionsPanel extends JPanel {
     private JSpinner sessionListLimitSpinner;
     /** Spinner for the hang-detection timeout in seconds (0 = disabled). */
     private JSpinner hangTimeoutSpinner;
+    /** Checkbox to enable MCP integration (pass --mcp-config flag). */
+    private javax.swing.JCheckBox mcpEnabledCheckBox;
 
     /** send-key radio buttons: value → button */
     private final Map<String, JRadioButton> sendRadios = new LinkedHashMap<>();
@@ -99,6 +101,7 @@ private void initComponents() {
 
         JTabbedPane tabs = new JTabbedPane();
         tabs.addTab("General", buildGeneralPanel());
+        tabs.addTab("Advanced", buildAdvancedPanel());
         tabs.addTab("Favorites", favoritesPanel);
         tabs.addTab("Profiles", profilesPanel);
         add(tabs, BorderLayout.CENTER);
@@ -181,16 +184,6 @@ private JPanel buildGeneralPanel() {
             newlineRadios.get(val).addActionListener(e -> syncExclusion(val, false));
         }
 
-        // --- debug mode ---
-        debugCheckBox = new javax.swing.JCheckBox("Debug mode (log all claude I/O to NetBeans log and output area)");
-        GridBagConstraints dbgGbc = new GridBagConstraints();
-        dbgGbc.gridx = 0; dbgGbc.gridy = row;
-        dbgGbc.gridwidth = 3;
-        dbgGbc.anchor = GridBagConstraints.WEST;
-        dbgGbc.insets = new Insets(4, 8, 4, 8);
-        form.add(debugCheckBox, dbgGbc);
-        row++;
-
         // --- diff in session ---
         diffInSessionCheck = new javax.swing.JCheckBox("Open diff in a separate tab");
         GridBagConstraints diffGbc = new GridBagConstraints();
@@ -229,18 +222,68 @@ private JPanel buildGeneralPanel() {
         form.add(sessionListLimitSpinner, gbc(1, row, false));
         row++;
 
+        // spacer
+        GridBagConstraints spacer = new GridBagConstraints();
+        spacer.gridx = 0; spacer.gridy = row;
+        spacer.gridwidth = 3; spacer.weighty = 1.0;
+        spacer.fill = GridBagConstraints.VERTICAL;
+        form.add(new JPanel(), spacer);
+
+        return form;
+    }
+
+    /**
+     * Builds the Advanced tab containing debug and hang-timeout settings.
+     *
+     * @return the Advanced tab panel
+     */
+    private JPanel buildAdvancedPanel() {
+        JPanel form = new JPanel(new GridBagLayout());
+        int row = 0;
+
+        // --- debug mode ---
+        debugCheckBox = new javax.swing.JCheckBox("Debug mode (log all claude I/O to NetBeans log and output area)");
+        GridBagConstraints dbgGbc = new GridBagConstraints();
+        dbgGbc.gridx = 0; dbgGbc.gridy = row;
+        dbgGbc.gridwidth = 2;
+        dbgGbc.anchor = GridBagConstraints.WEST;
+        dbgGbc.insets = new Insets(8, 8, 4, 8);
+        form.add(debugCheckBox, dbgGbc);
+        row++;
+
         // --- hang timeout ---
         form.add(new JLabel("Hang timeout (seconds, 0=disabled):"), gbc(0, row, false));
         hangTimeoutSpinner = new JSpinner(new SpinnerNumberModel(
                 ClaudeCodePreferences.DEFAULT_HANG_TIMEOUT_SECONDS, 0, 3600, 5));
         hangTimeoutSpinner.setToolTipText("Kill the process if no PTY output is received within this many seconds after launch (0 = disabled)");
-        form.add(hangTimeoutSpinner, gbc(1, row, false));
+        GridBagConstraints hangSpinnerGbc = gbc(1, row, false);
+        hangSpinnerGbc.weightx = 1.0;
+        form.add(hangTimeoutSpinner, hangSpinnerGbc);
+        row++;
+
+        // --- MCP enabled ---
+        mcpEnabledCheckBox = new javax.swing.JCheckBox("Enable MCP integration");
+        GridBagConstraints mcpGbc = new GridBagConstraints();
+        mcpGbc.gridx = 0; mcpGbc.gridy = row;
+        mcpGbc.gridwidth = 2;
+        mcpGbc.anchor = GridBagConstraints.WEST;
+        mcpGbc.insets = new Insets(12, 8, 0, 8);
+        form.add(mcpEnabledCheckBox, mcpGbc);
+        row++;
+
+        JLabel mcpDesc = new JLabel("<html><small>When disabled, the --mcp-config flag is not passed to claude. Hooks are always configured.</small></html>");
+        GridBagConstraints mcpDescGbc = new GridBagConstraints();
+        mcpDescGbc.gridx = 0; mcpDescGbc.gridy = row;
+        mcpDescGbc.gridwidth = 2;
+        mcpDescGbc.anchor = GridBagConstraints.WEST;
+        mcpDescGbc.insets = new Insets(0, 28, 4, 8);
+        form.add(mcpDesc, mcpDescGbc);
         row++;
 
         // spacer
         GridBagConstraints spacer = new GridBagConstraints();
         spacer.gridx = 0; spacer.gridy = row;
-        spacer.gridwidth = 3; spacer.weighty = 1.0;
+        spacer.gridwidth = 2; spacer.weighty = 1.0;
         spacer.fill = GridBagConstraints.VERTICAL;
         form.add(new JPanel(), spacer);
 
@@ -315,6 +358,7 @@ void load() {
                         == io.github.nbclaudecodegui.model.SessionMode.NEW);
         sessionListLimitSpinner.setValue(ClaudeCodePreferences.getSessionListLimit());
         hangTimeoutSpinner.setValue(ClaudeCodePreferences.getHangTimeoutSeconds());
+        mcpEnabledCheckBox.setSelected(ClaudeCodePreferences.isMcpEnabled());
 
         String sendVal    = ClaudeCodePreferences.getSendKey();
         String newlineVal = ClaudeCodePreferences.getNewlineKey();
@@ -348,6 +392,7 @@ void store() {
                         : io.github.nbclaudecodegui.model.SessionMode.CONTINUE_LAST);
         ClaudeCodePreferences.setSessionListLimit((Integer) sessionListLimitSpinner.getValue());
         ClaudeCodePreferences.setHangTimeoutSeconds((Integer) hangTimeoutSpinner.getValue());
+        ClaudeCodePreferences.setMcpEnabled(mcpEnabledCheckBox.isSelected());
         ClaudeCodePreferences.setSendKey(selectedValue(sendRadios));
         ClaudeCodePreferences.setNewlineKey(selectedValue(newlineRadios));
 

src/main/java/io/github/nbclaudecodegui/settings/ClaudeCodePreferences.java

@@ -525,6 +525,32 @@ public static void setHangTimeoutSeconds(int v) {
                 .putInt(KEY_HANG_TIMEOUT_SECONDS, Math.max(0, Math.min(3600, v)));
     }
 
+    // -------------------------------------------------------------------------
+    // mcpEnabled
+    // -------------------------------------------------------------------------
+
+    /** Preference key: pass {@code --mcp-config} flag to claude CLI. */
+    private static final String MCP_ENABLED = "mcpEnabled";
+
+    /**
+     * Returns whether MCP integration is enabled (default {@code true}).
+     *
+     * @return {@code true} to pass {@code --mcp-config}; {@code false} to skip it
+     */
+    public static boolean isMcpEnabled() {
+        return NbPreferences.forModule(ClaudeCodePreferences.class)
+                .getBoolean(MCP_ENABLED, true);
+    }
+
+    /**
+     * Persists the MCP-enabled flag.
+     *
+     * @param v {@code true} to enable MCP integration
+     */
+    public static void setMcpEnabled(boolean v) {
+        NbPreferences.forModule(ClaudeCodePreferences.class).putBoolean(MCP_ENABLED, v);
+    }
+
     private static String validated(String value, String fallback) {
         return ENTER.equals(value) || SHIFT_ENTER.equals(value)
                 || CTRL_ENTER.equals(value) || ALT_ENTER.equals(value)