chore: remove debugging infrastructure after permission fixes

Removes temporary debugging docs and excessive logging that were added to diagnose and fix permission modal issues.

Cleaned up:
- Deleted DEBUGGING.md (temporary troubleshooting guide)
- Deleted FIXES-2026-02-06.md (temporary fix summary)
- Removed debug logging from all Rust modules

src-tauri/src/achievements.rs

@@ -1671,7 +1671,7 @@ pub fn check_message_achievements(
     let mut newly_unlocked = Vec::new();
     let message_lower = message.to_lowercase();
 
-    println!("Checking message achievements for: {}", message);
+    tracing::info!("Checking message achievements for: {}", message);
 
     // Relationship & Greetings
     if message_lower.contains("good morning") && progress.unlock(AchievementId::GoodMorning) {
@@ -1863,18 +1863,18 @@ pub fn check_achievements(
 ) -> Vec<AchievementId> {
     let mut newly_unlocked = Vec::new();
 
-    println!(
+    tracing::info!(
         "Checking achievements with stats: messages={}, tokens={}, code_blocks={}",
         stats.messages_exchanged,
         stats.total_input_tokens + stats.total_output_tokens,
         stats.code_blocks_generated
     );
-    println!("Currently unlocked: {:?}", progress.unlocked);
+    tracing::info!("Currently unlocked: {:?}", progress.unlocked);
 
     // Token milestones
     let total_tokens = stats.total_input_tokens + stats.total_output_tokens;
     if total_tokens >= 1_000 && progress.unlock(AchievementId::FirstSteps) {
-        println!("Unlocked FirstSteps achievement!");
+        tracing::info!("Unlocked FirstSteps achievement!");
         newly_unlocked.push(AchievementId::FirstSteps);
     }
     if total_tokens >= 10_000 && progress.unlock(AchievementId::GrowingStrong) {
@@ -2244,7 +2244,7 @@ pub async fn save_achievements(
     // Create a serializable version with just the unlocked achievement IDs
     let unlocked_list: Vec<AchievementId> = progress.unlocked.iter().cloned().collect();
 
-    println!("Saving achievements: {:?}", unlocked_list);
+    tracing::info!("Saving achievements: {:?}", unlocked_list);
 
     store.set(
         "unlocked",
@@ -2252,18 +2252,18 @@ pub async fn save_achievements(
     );
     store.save().map_err(|e| e.to_string())?;
 
-    println!("Achievements saved successfully");
+    tracing::info!("Achievements saved successfully");
     Ok(())
 }
 
 // Load achievements from persistent store
 pub async fn load_achievements(app: &tauri::AppHandle) -> AchievementProgress {
-    println!("Loading achievements from store...");
+    tracing::info!("Loading achievements from store...");
 
     let store = match app.store("achievements.json") {
         Ok(s) => s,
         Err(e) => {
-            println!("Failed to open achievements store: {}", e);
+            tracing::error!("Failed to open achievements store: {}", e);
             return AchievementProgress::new();
         }
     };
@@ -2272,19 +2272,19 @@ pub async fn load_achievements(app: &tauri::AppHandle) -> AchievementProgress {
 
     // Get unlocked achievements
     if let Some(unlocked_value) = store.get("unlocked") {
-        println!("Found unlocked value in store: {:?}", unlocked_value);
+        tracing::info!("Found unlocked value in store: {:?}", unlocked_value);
         if let Ok(unlocked_list) =
             serde_json::from_value::<Vec<AchievementId>>(unlocked_value.clone())
         {
-            println!("Loaded {} achievements", unlocked_list.len());
+            tracing::info!("Loaded {} achievements", unlocked_list.len());
             for achievement_id in unlocked_list {
                 progress.unlocked.insert(achievement_id);
             }
         } else {
-            println!("Failed to parse unlocked achievements");
+            tracing::error!("Failed to parse unlocked achievements");
         }
     } else {
-        println!("No unlocked achievements found in store");
+        tracing::info!("No unlocked achievements found in store");
     }
 
     progress

src-tauri/src/discord_rpc.rs

@@ -30,7 +30,7 @@ impl DiscordRpcManager {
         if let Ok(app_data_dir) = app_handle.path().app_data_dir() {
             // Ensure the directory exists
             if let Err(e) = std::fs::create_dir_all(&app_data_dir) {
-                eprintln!("Failed to create app data directory: {}", e);
+                tracing::error!("Failed to create app data directory: {}", e);
                 return;
             }
             let log_path = app_data_dir.join("hikari_discord_rpc.log");

src-tauri/src/lib.rs

@@ -87,7 +87,7 @@ pub fn run() {
 
             // Set up system tray
             if let Err(e) = setup_tray(app.handle()) {
-                eprintln!("Failed to set up system tray: {}", e);
+                tracing::error!("Failed to set up system tray: {}", e);
             }
 
             // Handle window close event for minimize to tray and close confirmation

src-tauri/src/stats.rs

@@ -618,7 +618,7 @@ pub async fn save_stats(app: &tauri::AppHandle, stats: &UsageStats) -> Result<()
 
     let persisted = PersistedStats::from(stats);
 
-    println!("Saving stats: {:?}", persisted);
+    tracing::info!("Saving stats: {:?}", persisted);
 
     store.set(
         "lifetime_stats",
@@ -626,32 +626,32 @@ pub async fn save_stats(app: &tauri::AppHandle, stats: &UsageStats) -> Result<()
     );
     store.save().map_err(|e| e.to_string())?;
 
-    println!("Stats saved successfully");
+    tracing::info!("Stats saved successfully");
     Ok(())
 }
 
 /// Load lifetime stats from persistent store
 pub async fn load_stats(app: &tauri::AppHandle) -> Option<PersistedStats> {
-    println!("Loading stats from store...");
+    tracing::info!("Loading stats from store...");
 
     let store = match app.store("stats.json") {
         Ok(s) => s,
         Err(e) => {
-            println!("Failed to open stats store: {}", e);
+            tracing::error!("Failed to open stats store: {}", e);
             return None;
         }
     };
 
     if let Some(stats_value) = store.get("lifetime_stats") {
-        println!("Found lifetime stats in store: {:?}", stats_value);
+        tracing::info!("Found lifetime stats in store: {:?}", stats_value);
         if let Ok(persisted) = serde_json::from_value::<PersistedStats>(stats_value.clone()) {
-            println!("Loaded lifetime stats successfully");
+            tracing::info!("Loaded lifetime stats successfully");
             return Some(persisted);
         } else {
-            println!("Failed to parse lifetime stats");
+            tracing::error!("Failed to parse lifetime stats");
         }
     } else {
-        println!("No lifetime stats found in store");
+        tracing::info!("No lifetime stats found in store");
     }
 
     None

src-tauri/src/temp_manager.rs

@@ -77,8 +77,8 @@ impl TempFileManager {
             for file_path in files {
                 if file_path.exists() {
                     if let Err(e) = fs::remove_file(&file_path) {
-                        eprintln!(
-                            "Warning: Failed to remove temp file {:?}: {}",
+                        tracing::warn!(
+                            "Failed to remove temp file {:?}: {}",
                             file_path, e
                         );
                     }
@@ -115,7 +115,7 @@ impl TempFileManager {
             let path = entry.path();
             if path.is_file() && !tracked_files.contains(&path) {
                 if let Err(e) = fs::remove_file(&path) {
-                    eprintln!("Warning: Failed to remove orphaned file {:?}: {}", path, e);
+                    tracing::warn!("Failed to remove orphaned file {:?}: {}", path, e);
                 } else {
                     cleaned_count += 1;
                 }

src-tauri/src/wsl_bridge.rs

@@ -133,21 +133,21 @@ impl WslBridge {
         let app_clone = app.clone();
         let stats = self.stats.clone();
         tauri::async_runtime::spawn(async move {
-            println!("Loading saved achievements...");
+            tracing::info!("Loading saved achievements...");
             let achievements = crate::achievements::load_achievements(&app_clone).await;
-            println!(
+            tracing::info!(
                 "Loaded {} unlocked achievements",
                 achievements.unlocked.len()
             );
 
-            println!("Loading saved stats...");
+            tracing::info!("Loading saved stats...");
             let persisted_stats = crate::stats::load_stats(&app_clone).await;
 
             let mut stats_guard = stats.write();
             stats_guard.achievements = achievements;
 
             if let Some(persisted) = persisted_stats {
-                println!("Applying persisted lifetime stats");
+                tracing::info!("Applying persisted lifetime stats");
                 stats_guard.apply_persisted(persisted);
             }
         });
@@ -189,8 +189,8 @@ impl WslBridge {
 
         // Detect if we're running inside WSL or on Windows
         let is_wsl = detect_wsl();
-        eprintln!("[DEBUG] is_wsl: {}", is_wsl);
-        eprintln!("[DEBUG] options: {:?}", options);
+        tracing::debug!("is_wsl: {}", is_wsl);
+        tracing::debug!("options: {:?}", options);
 
         let mut command = if is_wsl {
             // Running inside WSL - call claude directly
@@ -199,8 +199,8 @@ impl WslBridge {
                 "Could not find claude binary. Is Claude Code installed?".to_string()
             })?;
 
-            eprintln!("[DEBUG] Found claude at: {}", claude_path);
-            eprintln!("[DEBUG] Working dir: {}", working_dir);
+            tracing::debug!("Found claude at: {}", claude_path);
+            tracing::debug!("Working dir: {}", working_dir);
 
             let mut cmd = Command::new(&claude_path);
             cmd.args([
@@ -256,7 +256,7 @@ impl WslBridge {
             cmd
         } else {
             // Running on Windows - use wsl with bash login shell to ensure PATH is loaded
-            eprintln!("[DEBUG] Windows path - using wsl");
+            tracing::debug!("Windows path - using wsl");
             let mut cmd = Command::new("wsl");
 
             // Build the claude command with all arguments
@@ -322,7 +322,7 @@ impl WslBridge {
             .stderr(Stdio::piped());
 
         let mut child = command.spawn().map_err(|e| {
-            eprintln!("[DEBUG] Spawn error: {:?}", e);
+            tracing::error!("Spawn error: {:?}", e);
             format!("Failed to spawn process: {}", e)
         })?;
 
@@ -500,7 +500,7 @@ impl WslBridge {
             (input_chars, stats.current_request_output_chars, stats.current_request_thinking_chars, stats.current_request_tools.clone(), model)
         };
 
-        println!("[COST ESTIMATION] Estimating cost for interrupted request");
+        tracing::info!("[COST ESTIMATION] Estimating cost for interrupted request");
 
         // Use conservative 3.5 chars/token for estimation (vs standard 4)
         let estimated_input_tokens = (input_chars as f64 / 3.5).ceil() as u64;
@@ -518,7 +518,7 @@ impl WslBridge {
                         let avg_tokens = (tool_stats.estimated_input_tokens + tool_stats.estimated_output_tokens)
                             / tool_stats.call_count;
                         tool_overhead_tokens += avg_tokens;
-                        println!("[COST ESTIMATION] Tool {} average: {} tokens", tool_name, avg_tokens);
+                        tracing::info!("[COST ESTIMATION] Tool {} average: {} tokens", tool_name, avg_tokens);
                     }
                 }
             }
@@ -532,9 +532,9 @@ impl WslBridge {
         let conservative_input = (total_estimated_input as f64 * safety_margin).ceil() as u64;
         let conservative_output = (total_estimated_output as f64 * safety_margin).ceil() as u64;
 
-        println!("[COST ESTIMATION] Input: {} chars → {} tokens (+ {} tool overhead) × 1.2 safety = {} tokens",
+        tracing::info!("[COST ESTIMATION] Input: {} chars → {} tokens (+ {} tool overhead) × 1.2 safety = {} tokens",
             input_chars, estimated_input_tokens, tool_overhead_tokens, conservative_input);
-        println!("[COST ESTIMATION] Output: {} chars → {} tokens × 1.2 safety = {} tokens",
+        tracing::info!("[COST ESTIMATION] Output: {} chars → {} tokens × 1.2 safety = {} tokens",
             output_chars + thinking_chars,
             estimated_output_tokens, conservative_output);
 
@@ -547,7 +547,7 @@ impl WslBridge {
             None,
         );
 
-        println!("[COST ESTIMATION] Estimated cost: ${:.4} (conservative)", estimated_cost);
+        tracing::info!("[COST ESTIMATION] Estimated cost: ${:.4} (conservative)", estimated_cost);
 
         // Add to stats with estimated flag
         {
@@ -587,11 +587,11 @@ impl WslBridge {
         let stats_snapshot = self.stats.read().clone();
         let app_clone = app.clone();
         tauri::async_runtime::spawn(async move {
-            println!("Saving stats on session stop...");
+            tracing::info!("Saving stats on session stop...");
             if let Err(e) = crate::stats::save_stats(&app_clone, &stats_snapshot).await {
-                eprintln!("Failed to save stats: {}", e);
+                tracing::error!("Failed to save stats: {}", e);
             } else {
-                println!("Stats saved successfully on session stop");
+                tracing::info!("Stats saved successfully on session stop");
             }
         });
 
@@ -636,11 +636,11 @@ fn handle_stdout(
         match line {
             Ok(line) if !line.is_empty() => {
                 if let Err(e) = process_json_line(&line, &app, &stats, &conversation_id) {
-                    eprintln!("Error processing line: {}", e);
+                    tracing::error!("Error processing line: {}", e);
                 }
             }
             Err(e) => {
-                eprintln!("Error reading stdout: {}", e);
+                tracing::error!("Error reading stdout: {}", e);
                 break;
             }
             _ => {}
@@ -663,7 +663,7 @@ fn handle_stderr(
                 // Check if this is a SubagentStart hook message
                 if line.contains("[SubagentStart Hook]") {
                     if let Some(agent_data) = parse_subagent_start_hook(&line) {
-                        eprintln!("[DEBUG] Parsed SubagentStart hook: agent_id={}, parent={:?}",
+                        tracing::debug!("Parsed SubagentStart hook: agent_id={}, parent={:?}",
                             agent_data.agent_id, agent_data.parent_tool_use_id);
 
                         // Emit an agent-update event with the agent_id
@@ -815,7 +815,7 @@ fn process_json_line(
                     let stats_guard = stats.read();
                     stats_guard.model.clone()
                 }).unwrap_or_else(|| {
-                    println!("[WARNING] No model info available for cost calculation, using default");
+                    tracing::warn!("No model info available for cost calculation, using default");
                     "claude-sonnet-4-5-20250929".to_string()
                 });
 
@@ -828,7 +828,7 @@ fn process_json_line(
                     usage.cache_read_input_tokens,
                 );
 
-                println!("Assistant message tokens - input: {}, output: {}, cache_creation: {:?}, cache_read: {:?}, cost: ${:.4}",
+                tracing::info!("Assistant message tokens - input: {}, output: {}, cache_creation: {:?}, cache_read: {:?}, cost: ${:.4}",
                     usage.input_tokens,
                     usage.output_tokens,
                     usage.cache_creation_input_tokens,
@@ -917,8 +917,8 @@ fn process_json_line(
                                 .unwrap_or_default()
                                 .as_millis() as u64;
 
-                            eprintln!(
-                                "[DEBUG] Emitting agent-start: id={}, desc={}, type={}, parent={:?}",
+                            tracing::debug!(
+                                "Emitting agent-start: id={}, desc={}, type={}, parent={:?}",
                                 id, description, subagent_type, parent_tool_use_id
                             );
 
@@ -1063,6 +1063,13 @@ fn process_json_line(
             duration_ms,
             num_turns,
         } => {
+            tracing::info!(
+                "Received Result message: subtype={}, has_denials={}, denial_count={:?}",
+                subtype,
+                permission_denials.is_some(),
+                permission_denials.as_ref().map(|d| d.len())
+            );
+
             let state = if subtype == "success" {
                 CharacterState::Success
             } else {
@@ -1078,12 +1085,18 @@ fn process_json_line(
                 tools
             });
 
+            tracing::debug!(
+                "Captured {} pending tool use(s): {:?}",
+                captured_pending_tools.len(),
+                captured_pending_tools.iter().map(|t| &t.tool_name).collect::<Vec<_>>()
+            );
+
             // Log turn metrics if available
             if let Some(duration) = duration_ms {
-                println!("Turn completed in {}ms", duration);
+                tracing::info!("Turn completed in {}ms", duration);
             }
             if let Some(turns) = num_turns {
-                println!("Turn count: {}", turns);
+                tracing::info!("Turn count: {}", turns);
             }
 
             // Track token usage from Result messages if available
@@ -1113,7 +1126,7 @@ fn process_json_line(
                     usage_info.cache_creation_input_tokens,
                     usage_info.cache_read_input_tokens,
                 );
-                println!("Result message tokens - input: {}, output: {}, cache_creation: {:?}, cache_read: {:?}",
+                tracing::info!("Result message tokens - input: {}, output: {}, cache_creation: {:?}, cache_read: {:?}",
                     usage_info.input_tokens,
                     usage_info.output_tokens,
                     usage_info.cache_creation_input_tokens,
@@ -1143,9 +1156,9 @@ fn process_json_line(
             let newly_unlocked = {
                 let mut stats_guard = stats.write();
                 stats_guard.get_session_duration();
-                println!("Checking achievements after result message...");
+                tracing::info!("Checking achievements after result message...");
                 let unlocked = stats_guard.check_achievements();
-                println!("Newly unlocked achievements: {:?}", unlocked);
+                tracing::info!("Newly unlocked achievements: {:?}", unlocked);
                 unlocked
             };
 
@@ -1160,20 +1173,20 @@ fn process_json_line(
 
             // Save achievements after unlocking new ones
             if !newly_unlocked.is_empty() {
-                println!("Saving newly unlocked achievements: {:?}", newly_unlocked);
+                tracing::info!("Saving newly unlocked achievements: {:?}", newly_unlocked);
                 let app_handle = app.clone();
                 let achievements_progress = stats.read().achievements.clone();
 
                 // Use Tauri's async runtime instead of tokio::spawn
                 tauri::async_runtime::spawn(async move {
-                    println!("Spawned save task for achievements");
+                    tracing::info!("Spawned save task for achievements");
                     if let Err(e) =
                         crate::achievements::save_achievements(&app_handle, &achievements_progress)
                             .await
                     {
-                        eprintln!("Failed to save achievements: {}", e);
+                        tracing::error!("Failed to save achievements: {}", e);
                     } else {
-                        println!("Achievement save task completed successfully");
+                        tracing::info!("Achievement save task completed successfully");
                     }
                 });
             }
@@ -1190,9 +1203,9 @@ fn process_json_line(
             {
                 let app_handle = app.clone();
                 tauri::async_runtime::spawn(async move {
-                    println!("Periodic stats save (every 10 messages)...");
+                    tracing::info!("Periodic stats save (every 10 messages)...");
                     if let Err(e) = crate::stats::save_stats(&app_handle, &current_stats).await {
-                        eprintln!("Failed to save stats: {}", e);
+                        tracing::error!("Failed to save stats: {}", e);
                     }
                 });
             }
@@ -1218,12 +1231,6 @@ fn process_json_line(
             if let Some(denials) = permission_denials {
                 // Only process if there are actually denials
                 if !denials.is_empty() {
-                    // Skip permission prompts if the result was successful - tools were already approved
-                    if subtype == "success" {
-                        emit_state_change(app, state, None, conversation_id.clone());
-                        return Ok(());
-                    }
-
                     let mut regular_permission_requests = Vec::new();
 
                     // Get denied tool IDs for later comparison
@@ -1433,7 +1440,7 @@ fn process_json_line(
             // Check achievements after user message
             let newly_unlocked = {
                 let mut stats_guard = stats.write();
-                println!("User sent message, checking achievements...");
+                tracing::info!("User sent message, checking achievements...");
 
                 // Check message-based achievements
                 let mut unlocked = crate::achievements::check_message_achievements(
@@ -1450,7 +1457,7 @@ fn process_json_line(
 
             // Emit achievement events for any newly unlocked achievements
             for achievement_id in &newly_unlocked {
-                println!("User message unlocked achievement: {:?}", achievement_id);
+                tracing::info!("User message unlocked achievement: {:?}", achievement_id);
                 let info = get_achievement_info(achievement_id);
                 let _ = app.emit(
                     "achievement:unlocked",
@@ -1460,7 +1467,7 @@ fn process_json_line(
 
             // Save achievements after unlocking new ones
             if !newly_unlocked.is_empty() {
-                println!("Saving newly unlocked achievements from user message");
+                tracing::info!("Saving newly unlocked achievements from user message");
                 let app_handle = app.clone();
                 let achievements_progress = stats.read().achievements.clone();
                 tauri::async_runtime::spawn(async move {
@@ -1468,9 +1475,9 @@ fn process_json_line(
                         crate::achievements::save_achievements(&app_handle, &achievements_progress)
                             .await
                     {
-                        eprintln!("Failed to save achievements: {}", e);
+                        tracing::error!("Failed to save achievements: {}", e);
                     } else {
-                        println!("Achievements saved after user message");
+                        tracing::info!("Achievements saved after user message");
                     }
                 });
             }

src-tauri/src/wsl_notifications.rs

@@ -48,15 +48,15 @@ $notifier.Show($toast)
     match output {
         Ok(result) => {
             if result.status.success() {
-                println!("WSL notification sent successfully");
+                tracing::info!("WSL notification sent successfully");
                 return Ok(());
             } else {
                 let stderr = String::from_utf8_lossy(&result.stderr);
-                println!("PowerShell toast failed: {}", stderr);
+                tracing::error!("PowerShell toast failed: {}", stderr);
             }
         }
         Err(e) => {
-            println!("Failed to run PowerShell: {}", e);
+            tracing::error!("Failed to run PowerShell: {}", e);
         }
     }
 
@@ -74,7 +74,7 @@ $notifier.Show($toast)
 
     if let Ok(result) = notify_result {
         if result.status.success() {
-            println!("Notification sent via wsl-notify-send");
+            tracing::info!("Notification sent via wsl-notify-send");
             return Ok(());
         }
     }