diff --git a/src-tauri/src/lib.rs b/src-tauri/src/lib.rs
index 68a8046..9d0de54 100644
--- a/src-tauri/src/lib.rs
+++ b/src-tauri/src/lib.rs
@@ -165,12 +165,19 @@ pub fn run() {
                 .build(),
         )
         .setup(|app| {
-            // Clean up orphaned tmp files from previous crashes
-            {
-                use data::beads::RealBeadsCli;
-                use data::bridge::Bridge;
-                use data::lore::RealLoreCli;
+            use data::beads::RealBeadsCli;
+            use data::bridge::Bridge;
+            use data::lore::RealLoreCli;
 
+            // 1. Ensure data directories exist
+            let config = app::AppConfig::default();
+            if let Err(e) = app::ensure_data_dir(&config) {
+                tracing::error!("Failed to create data directory: {}", e);
+                // Continue anyway - commands will fail gracefully
+            }
+
+            // 2. Clean up orphaned tmp files from previous crashes
+            {
                 let bridge: Bridge<RealLoreCli, RealBeadsCli> =
                     Bridge::new(RealLoreCli, RealBeadsCli);
                 if let Err(e) = bridge.cleanup_tmp_files() {
@@ -178,6 +185,49 @@ pub fn run() {
                 }
             }
 
+            // 3. Verify CLI dependencies (async, spawned to not block startup)
+            let app_handle = app.handle().clone();
+            tauri::async_runtime::spawn(async move {
+                let (cli_available, warnings) = app::verify_cli_dependencies().await;
+
+                // Log warnings
+                for warning in &warnings {
+                    match warning {
+                        app::StartupWarning::LoreMissing => {
+                            tracing::warn!("lore CLI not found - GitLab sync will be unavailable");
+                        }
+                        app::StartupWarning::BrMissing => {
+                            tracing::warn!("br CLI not found - beads integration will be unavailable");
+                        }
+                        app::StartupWarning::BvMissing => {
+                            tracing::warn!("bv CLI not found - triage features will be unavailable");
+                        }
+                        _ => {}
+                    }
+                }
+
+                // Emit startup warnings to frontend
+                if !warnings.is_empty() {
+                    if let Err(e) = app_handle.emit("startup-warnings", &warnings) {
+                        tracing::error!("Failed to emit startup warnings: {}", e);
+                    }
+                }
+
+                // Emit CLI availability to frontend
+                if let Err(e) = app_handle.emit("cli-availability", &cli_available) {
+                    tracing::error!("Failed to emit CLI availability: {}", e);
+                }
+
+                // 4. Trigger startup reconciliation if CLIs are available
+                if cli_available.lore && cli_available.br {
+                    tracing::info!("Triggering startup reconciliation");
+                    // The frontend will call reconcile() command when ready
+                    if let Err(e) = app_handle.emit("startup-sync-ready", ()) {
+                        tracing::error!("Failed to emit startup-sync-ready: {}", e);
+                    }
+                }
+            });
+
             // Set up system tray
             if let Err(e) = setup_tray(app) {
                 tracing::error!("Failed to setup system tray: {}", e);