MCP Fixes

Author: stephanj

src/main/java/com/devoxx/genie/service/analyzer/DevoxxGenieGenerator.java

@@ -114,7 +114,7 @@ public void generate() {
         indicator.setText("Scanning project structure...");
         indicator.setIndeterminate(true);
 
-        // Initialize FileScanner's gitignore parser
+        // Initialize FileScanner's gitignore parser - runs in read action internally now
         fileScanner.initGitignoreParser(project, baseDir);
 
         // Get ProjectFileIndex for file traversal

src/main/java/com/devoxx/genie/service/projectscanner/FileScanner.java

@@ -3,10 +3,13 @@
 import com.devoxx.genie.model.ScanContentResult;
 import com.devoxx.genie.service.DevoxxGenieSettingsService;
 import com.devoxx.genie.ui.settings.DevoxxGenieStateService;
+import com.devoxx.genie.ui.util.NotificationUtil;
+import com.intellij.openapi.application.ApplicationManager;
 import com.intellij.openapi.project.Project;
 import com.intellij.openapi.project.ProjectUtil;
 import com.intellij.openapi.roots.ProjectFileIndex;
 import com.intellij.openapi.roots.ProjectRootManager;
+import com.intellij.openapi.util.Computable;
 import com.intellij.openapi.vfs.VfsUtilCore;
 import com.intellij.openapi.vfs.VirtualFile;
 import com.intellij.openapi.vfs.VirtualFileVisitor;
@@ -64,7 +67,7 @@ public void initGitignoreParser(Project project, VirtualFile startDirectory) {
         if (startDirectory == null) {
             // Use project base path when no specific directory is provided
             projectBasePath = project.getBasePath();
-            log.info("Using project base path as startDirectory is null: " + projectBasePath);
+            log.info("Using project base path as startDirectory is null: {}", projectBasePath);
         } else {
             projectBasePath = determineCorrectProjectBaseDir(project, startDirectory);
         }
@@ -74,20 +77,28 @@ public void initGitignoreParser(Project project, VirtualFile startDirectory) {
             return;
         }
 
-        log.info("Initializing GitIgnore parser with resolved project base directory: " + projectBasePath);
+        log.info("Initializing GitIgnore parser with resolved project base directory: {}", projectBasePath);
         this.gitIgnoreFileSet = new GitIgnoreFileSet(new File(projectBasePath), false);
 
-        collectGitignoreFiles(startDirectory);
+        if (startDirectory == null) {
+            log.error("The start directory for the file scanner is null");
+            NotificationUtil.sendNotification(project, "The start directory for the file scanner is null");
+        } else {
+            collectGitignoreFiles(startDirectory);
+        }
     }
 
     /**
      * Determines the most appropriate base directory, considering project modules (workspaces).
      */
     private @Nullable String determineCorrectProjectBaseDir(@NotNull Project project, @NotNull VirtualFile startDirectory) {
         // First check if startDirectory belongs to an explicit module's content root
-        ProjectFileIndex fileIndex = ProjectRootManager.getInstance(project).getFileIndex();
-
-        VirtualFile contentRoot = fileIndex.getContentRootForFile(startDirectory);
+        // Wrap file index access in a read action to prevent threading issues
+        VirtualFile contentRoot = ApplicationManager.getApplication().runReadAction((Computable<VirtualFile>) () -> {
+            ProjectFileIndex fileIndex = ProjectRootManager.getInstance(project).getFileIndex();
+            return fileIndex.getContentRootForFile(startDirectory);
+        });
+        
         if (contentRoot != null) {
             log.info("Content root determined from workspace (module): " + contentRoot.getPath());
             return contentRoot.getPath();
@@ -180,7 +191,8 @@ public boolean visitFile(@NotNull VirtualFile file) {
                     }
                 } else {
                     log.info("Checking file: " + file.getPath());
-                    boolean isInContent = fileIndex.isInContent(file);
+                    // Wrap file index access in a read action to prevent threading issues
+                    boolean isInContent = ApplicationManager.getApplication().runReadAction((Computable<Boolean>) () -> fileIndex.isInContent(file));
                     boolean shouldNotExclude = !shouldExcludeFile(file);
                     boolean shouldInclude = shouldIncludeFile(file);
                     log.info("File checks: isInContent=" + isInContent + ", shouldNotExclude=" + shouldNotExclude + ", shouldInclude=" + shouldInclude);
@@ -213,7 +225,9 @@ public boolean visitFile(@NotNull VirtualFile file) {
      * @return the reason for skipping the file
      */
     private String determineSkipReason(VirtualFile file, ProjectFileIndex fileIndex) {
-        if (!fileIndex.isInContent(file)) {
+        // Wrap file index access in a read action to prevent threading issues
+        boolean isInContent = ApplicationManager.getApplication().runReadAction((Computable<Boolean>) () -> fileIndex.isInContent(file));
+        if (!isInContent) {
             return "not in project content";
         }
 

src/main/java/com/devoxx/genie/ui/MCPLogToolWindowFactory.java

@@ -1,5 +1,6 @@
 package com.devoxx.genie.ui;
 
+import com.devoxx.genie.service.mcp.MCPService;
 import com.devoxx.genie.ui.panel.mcp.MCPLogPanel;
 import com.intellij.openapi.project.Project;
 import com.intellij.openapi.wm.ToolWindow;
@@ -31,7 +32,7 @@ public void createToolWindowContent(@NotNull Project project, @NotNull ToolWindo
     public boolean shouldBeAvailable(@NotNull Project project) {
         // Only show this tool window when MCP is enabled
         // When enabled the user can turn on/off MCP logging
-        return com.devoxx.genie.service.mcp.MCPService.isMCPEnabled();
+        return MCPService.isMCPEnabled();
     }
 
     @Override

src/main/java/com/devoxx/genie/ui/panel/ActionButtonsPanel.java

@@ -26,15 +26,17 @@
 import com.intellij.openapi.ui.popup.JBPopup;
 import com.intellij.openapi.ui.popup.JBPopupFactory;
 import com.intellij.openapi.vfs.VirtualFile;
-import com.intellij.ui.components.JBList;
-import com.intellij.ui.components.JBScrollPane;
+import com.intellij.openapi.wm.ToolWindow;
+import com.intellij.openapi.wm.ToolWindowManager;
 import lombok.Getter;
 import org.jetbrains.annotations.NotNull;
 
 import javax.swing.*;
-import javax.swing.event.MouseInputAdapter;
 import java.awt.*;
+import com.intellij.ui.components.JBList;
+import com.intellij.ui.components.JBScrollPane;
 import java.awt.event.ActionEvent;
+import javax.swing.event.MouseInputAdapter;
 import java.awt.event.MouseEvent;
 import java.util.ArrayList;
 import java.util.Comparator;
@@ -120,7 +122,7 @@ private void createMCPToolsCounter() {
         mcpToolsCountLabel.setIconTextGap(4);
         mcpToolsCountLabel.setCursor(Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
 
-        // Add click listener for showing the tool list popup
+        // Add click listener for showing the tool list popup or opening the MCP logs panel
         mcpToolsCountLabel.addMouseListener(new MouseInputAdapter() {
             @Override
             public void mouseClicked(MouseEvent e) {

src/main/java/com/devoxx/genie/ui/settings/mcp/dialog/MCPServerDialog.java

@@ -63,7 +63,7 @@ public MCPServerDialog(MCPServer existingServer) {
         gbc.fill = GridBagConstraints.HORIZONTAL;
         gbc.insets = new Insets(5, 5, 5, 5);
 
-        // Reset gridwidth for remaining components
+        // Reset grid width for remaining components
         gbc.gridwidth = 1;
 
         // Name field
@@ -197,7 +197,7 @@ private void testConnectionAndFetchTools() {
             StdioMcpTransport transport = new StdioMcpTransport.Builder()
                     .command(mcpCommand)
                     .environment(env)
-                    .logEvents(true)
+                    .logEvents(false)
                     .build();
 
             McpClient mcpClient = new DefaultMcpClient.Builder()

src/main/resources/META-INF/plugin.xml

@@ -609,8 +609,10 @@
         <toolWindow id="DevoxxGenieMCPLogs"
                     anchor="bottom"
                     icon="/icons/logIcon.svg"
-                    factoryClass="com.devoxx.genie.ui.MCPLogToolWindowFactory"
-                    canCloseContents="true"/>
+                    secondary="true"
+                    doNotActivateOnStart="true"
+                    canCloseContents="true"
+                    factoryClass="com.devoxx.genie.ui.MCPLogToolWindowFactory"/>
 
         <applicationService serviceImplementation="com.devoxx.genie.ui.settings.DevoxxGenieStateService"/>
         <applicationService serviceImplementation="com.devoxx.genie.service.conversations.ConversationStorageService"/>