diff --git a/src/bin/semcode-mcp.rs b/src/bin/semcode-mcp.rs
index 8ef5ead..86b2246 100644
--- a/src/bin/semcode-mcp.rs
+++ b/src/bin/semcode-mcp.rs
@@ -2090,6 +2090,7 @@ impl McpServer {
             "initialize" => self.handle_initialize(params).await,
             "tools/list" => self.handle_list_tools().await,
             "tools/call" => self.handle_tool_call(params).await,
+            "ping" => json!({}),
             _ => json!({
                 "error": {
                     "code": -32601,
@@ -5086,20 +5087,38 @@ async fn run_stdio_server(server: Arc<McpServer>) -> Result<()> {
 
                 match serde_json::from_str::<Value>(&line) {
                     Ok(request) => {
-                        let response = server.handle_request(request).await;
-                        if let Ok(response_str) = serde_json::to_string(&response) {
-                            let mut stdout_guard = stdout.lock().await;
-                            if let Err(e) = stdout_guard.write_all(response_str.as_bytes()).await {
-                                eprintln!("Failed to write response: {e}");
-                                break;
-                            }
-                            if let Err(e) = stdout_guard.write_all(b"\n").await {
-                                eprintln!("Failed to write newline: {e}");
-                                break;
+                        // Check if this is a notification (no id) or a request (has id)
+                        if request.get("id").is_some() {
+                            // It's a request, send a response
+                            let response = server.handle_request(request).await;
+                            if let Ok(response_str) = serde_json::to_string(&response) {
+                                let mut stdout_guard = stdout.lock().await;
+                                if let Err(e) = stdout_guard.write_all(response_str.as_bytes()).await {
+                                    eprintln!("Failed to write response: {e}");
+                                    break;
+                                }
+                                if let Err(e) = stdout_guard.write_all(b"\n").await {
+                                    eprintln!("Failed to write newline: {e}");
+                                    break;
+                                }
+                                if let Err(e) = stdout_guard.flush().await {
+                                    eprintln!("Failed to flush stdout: {e}");
+                                    break;
+                                }
                             }
-                            if let Err(e) = stdout_guard.flush().await {
-                                eprintln!("Failed to flush stdout: {e}");
-                                break;
+                        } else {
+                            // It's a notification, handle without response
+                            let method = request["method"].as_str().unwrap_or("");
+                            match method {
+                                "notifications/initialized" => {
+                                    eprintln!("Client initialized");
+                                }
+                                "notifications/cancelled" => {
+                                    eprintln!("Request cancelled (notification received)");
+                                }
+                                _ => {
+                                    eprintln!("Received notification: {}", method);
+                                }
                             }
                         }
                     }
@@ -5159,9 +5178,6 @@ async fn main() -> Result<()> {
     // Create MCP server
     let server = Arc::new(McpServer::new(&database_path, &args.git_repo, args.model_path).await?);
 
-    // Ensure tables exist
-    server.db.create_tables().await?;
-
     // Spawn background task to index current commit if needed
     eprintln!("[Background] Spawning background indexing task");
     let db_for_indexing = server.db.clone();
@@ -5169,6 +5185,11 @@ async fn main() -> Result<()> {
     let indexing_state_for_bg = server.indexing_state.clone();
     let notification_tx_for_bg = server.notification_tx.clone();
     let _indexing_handle = tokio::spawn(async move {
+        // Ensure tables exist before indexing
+        if let Err(e) = db_for_indexing.create_tables().await {
+            eprintln!("[Background] Error creating/verifying tables: {}", e);
+        }
+
         index_current_commit_background(
             db_for_indexing,
             git_repo_for_indexing,
diff --git a/src/database/connection.rs b/src/database/connection.rs
index eccc360..409bc5d 100644
--- a/src/database/connection.rs
+++ b/src/database/connection.rs
@@ -1966,7 +1966,7 @@ impl DatabaseManager {
     pub async fn optimize_database(&self) -> Result<()> {
         use colored::Colorize;
 
-        println!(
+        tracing::info!(
             "\n{}",
             "═══ DATABASE OPTIMIZATION STARTED ═══".yellow().bold()
         );
@@ -1974,22 +1974,22 @@ impl DatabaseManager {
         tracing::info!("Running database optimization...");
 
         // Rebuild all scalar indices to ensure they're optimal
-        println!("{}", "  → Rebuilding scalar indices...".cyan());
+        tracing::info!("{}", "  → Rebuilding scalar indices...".cyan());
         self.rebuild_indices().await?;
-        println!("{}", "  ✓ Scalar indices rebuilt".green());
+        tracing::info!("{}", "  ✓ Scalar indices rebuilt".green());
 
         // Run table optimization
-        println!("{}", "  → Optimizing tables...".cyan());
+        tracing::info!("{}", "  → Optimizing tables...".cyan());
         self.optimize_tables().await?;
-        println!("{}", "  ✓ Tables optimized".green());
+        tracing::info!("{}", "  ✓ Tables optimized".green());
 
         // Compact and cleanup (triggers compression)
-        println!("{}", "  → Compacting and pruning old versions...".cyan());
+        tracing::info!("{}", "  → Compacting and pruning old versions...".cyan());
         self.compact_and_cleanup().await?;
-        println!("{}", "  ✓ Compaction complete".green());
+        tracing::info!("{}", "  ✓ Compaction complete".green());
 
         let elapsed = start_time.elapsed();
-        println!(
+        tracing::info!(
             "{}",
             format!(
                 "═══ DATABASE OPTIMIZATION COMPLETE ({:.1}s) ═══\n",
diff --git a/src/git_range.rs b/src/git_range.rs
index 988393a..06a0aae 100644
--- a/src/git_range.rs
+++ b/src/git_range.rs
@@ -749,7 +749,7 @@ pub async fn process_git_range(
     let commit_count = commit_shas.len();
 
     if !commit_shas.is_empty() {
-        println!(
+        info!(
             "Checking for {} commits already in database...",
             commit_count
         );
@@ -768,13 +768,13 @@ pub async fn process_git_range(
 
         let already_indexed = commit_count - new_commit_shas.len();
         if already_indexed > 0 {
-            println!(
+            info!(
                 "{} commits already indexed, processing {} new commits",
                 already_indexed,
                 new_commit_shas.len()
             );
         } else {
-            println!("Processing all {} new commits", new_commit_shas.len());
+            info!("Processing all {} new commits", new_commit_shas.len());
         }
 
         if !new_commit_shas.is_empty() {
@@ -799,7 +799,7 @@ pub async fn process_git_range(
                 commit_extraction_start.elapsed().as_secs_f64()
             );
         } else {
-            println!("All commits in range are already indexed!");
+            info!("All commits in range are already indexed!");
         }
     } else {
         info!("No commits found in range");
@@ -843,24 +843,24 @@ pub async fn process_git_range(
 
     let total_time = start_time.elapsed();
 
-    println!("\n=== Git Range Pipeline Complete ===");
-    println!("Total time: {:.1}s", total_time.as_secs_f64());
-    println!("Commits indexed: {commit_count}");
-    println!("Files processed: {}", stats.files_processed);
-    println!("Functions indexed: {}", stats.functions_count);
-    println!("Types indexed: {}", stats.types_count);
+    info!("\n=== Git Range Pipeline Complete ===");
+    info!("Total time: {:.1}s", total_time.as_secs_f64());
+    info!("Commits indexed: {commit_count}");
+    info!("Files processed: {}", stats.files_processed);
+    info!("Functions indexed: {}", stats.functions_count);
+    info!("Types indexed: {}", stats.types_count);
 
     // Check if optimization is needed after git range indexing
     match db_manager.check_optimization_health().await {
         Ok((needs_optimization, message)) => {
             if needs_optimization {
-                println!("\n{}", message);
+                info!("\n{}", message);
                 match db_manager.optimize_database().await {
-                    Ok(_) => println!("Database optimization completed successfully"),
+                    Ok(_) => info!("Database optimization completed successfully"),
                     Err(e) => error!("Failed to optimize database: {}", e),
                 }
             } else {
-                println!("\n{}", message);
+                info!("\n{}", message);
             }
         }
         Err(e) => {
diff --git a/src/indexer.rs b/src/indexer.rs
index f0ecb9e..266498f 100644
--- a/src/indexer.rs
+++ b/src/indexer.rs
@@ -53,14 +53,14 @@ pub async fn check_and_optimize_if_needed(
     match db_manager.check_optimization_health().await {
         Ok((needs_optimization, message)) => {
             if needs_optimization {
-                println!("{}", message);
-                println!(
+                info!("{}", message);
+                info!(
                     "\n{} Fragment threshold exceeded during indexing, running optimization...",
                     "⚠️".yellow()
                 );
                 match db_manager.optimize_database().await {
                     Ok(_) => {
-                        println!("{} In-progress optimization completed", "✓".green());
+                        info!("{} In-progress optimization completed", "✓".green());
                     }
                     Err(e) => {
                         warn!("In-progress optimization failed: {}", e);
@@ -1027,11 +1027,11 @@ pub async fn index_git_commits(
     let commit_count = commit_shas.len();
 
     if commit_shas.is_empty() {
-        println!("No commits found in range: {}", git_range);
+        info!("No commits found in range: {}", git_range);
         return Ok(0);
     }
 
-    println!(
+    info!(
         "Checking for {} commits already in database...",
         commit_count
     );
@@ -1050,17 +1050,17 @@ pub async fn index_git_commits(
 
     let already_indexed = commit_count - new_commit_shas.len();
     if already_indexed > 0 {
-        println!(
+        info!(
             "{} commits already indexed, processing {} new commits",
             already_indexed,
             new_commit_shas.len()
         );
     } else {
-        println!("Processing all {} new commits", new_commit_shas.len());
+        info!("Processing all {} new commits", new_commit_shas.len());
     }
 
     if new_commit_shas.is_empty() {
-        println!("All commits in range are already indexed!");
+        info!("All commits in range are already indexed!");
         return Ok(commit_count);
     }
 
@@ -1083,9 +1083,9 @@ pub async fn index_git_commits(
 
     let total_time = start_time.elapsed();
 
-    println!("\n=== Commit Indexing Complete ===");
-    println!("Total time: {:.1}s", total_time.as_secs_f64());
-    println!("Commits indexed: {}", commit_count);
+    info!("\n=== Commit Indexing Complete ===");
+    info!("Total time: {:.1}s", total_time.as_secs_f64());
+    info!("Commits indexed: {}", commit_count);
 
     Ok(commit_count)
 }
diff --git a/src/lib.rs b/src/lib.rs
index 38db987..d3804ad 100644
--- a/src/lib.rs
+++ b/src/lib.rs
@@ -81,6 +81,9 @@ pub mod logging {
                 .add_directive("DatasetRecordBatchStream=error".parse().unwrap());
         }
 
-        tracing_subscriber::fmt().with_env_filter(env_filter).init();
+        tracing_subscriber::fmt()
+            .with_env_filter(env_filter)
+            .with_writer(std::io::stderr)
+            .init();
     }
 }