fix: resolve message submission and stuck processing bugs (#199)

## Summary

- **Fix `isProcessing` tracking**: The `isProcessing` store field was initialised as `false` and never set to `true` in production, making all submission guards no-ops. Now `setProcessing(true)` is called after `send_prompt` succeeds in both `handleSubmit` and `handleQuickAction`, and `setProcessingForConversation(id, false)` is called when the backend emits an idle/success/error state.
- **Fix auto-granted tools dropped on permission reconnect** (closes #198): `PermissionModal.svelte` was passing only session-granted tools when reconnecting after a permission approval, silently dropping `config.auto_granted_tools`. Fixed to merge both sets, matching the behaviour of every other `start_claude` call site.
- **Add mid-session watchdog**: A watchdog thread now kills the Claude Code process if a user message is sent but no `Result` arrives within 5 minutes. This triggers the existing disconnect/error flow so the user is notified and can reconnect. A generation counter ensures watchdogs from previous sessions exit cleanly when a new session starts.

## Test plan

- [ ] Send a message and verify the textarea is disabled and the stop button is visible while Claude is processing
- [ ] Verify the textarea re-enables after Claude finishes responding
- [ ] Enable a tool in default permissions (e.g. Read), start a session, trigger a permission approval for another tool, approve it — verify the previously auto-granted tool is no longer re-prompted
- [ ] Verify all existing tests pass (`./check-all.sh`)

✨ This PR was created with help from Hikari~ 🌸

Reviewed-on: #199
Co-authored-by: Hikari <hikari@nhcarrigan.com>
Co-committed-by: Hikari <hikari@nhcarrigan.com>

src-tauri/src/wsl_bridge.rs

@@ -1,9 +1,9 @@
 use std::io::{BufRead, BufReader, Write};
 use std::process::{Child, ChildStdin, Command, Stdio};
-use std::sync::atomic::{AtomicBool, Ordering};
+use std::sync::atomic::{AtomicBool, AtomicU64, Ordering};
 use std::sync::Arc;
 use std::thread;
-use std::time::{Duration, SystemTime, UNIX_EPOCH};
+use std::time::{Duration, Instant, SystemTime, UNIX_EPOCH};
 use parking_lot::Mutex;
 use tauri::{AppHandle, Emitter};
 use tempfile::NamedTempFile;
@@ -114,6 +114,11 @@ pub struct WslBridge {
     /// Set to true by stop()/interrupt() before killing the process so handle_stdout knows
     /// the disconnect was intentional and should not emit a second Disconnected event.
     intentional_stop: Arc<AtomicBool>,
+    /// Tracks when the most recent user message was sent. Cleared when a `Result` message
+    /// arrives. The mid-session watchdog uses this to detect a stuck process.
+    pending_since: Arc<Mutex<Option<Instant>>>,
+    /// Incremented each time `start()` is called so each session's watchdog knows when to exit.
+    watchdog_generation: Arc<AtomicU64>,
 }
 
 impl WslBridge {
@@ -128,6 +133,8 @@ impl WslBridge {
             conversation_id: None,
             received_init: Arc::new(AtomicBool::new(false)),
             intentional_stop: Arc::new(AtomicBool::new(false)),
+            pending_since: Arc::new(Mutex::new(None)),
+            watchdog_generation: Arc::new(AtomicU64::new(0)),
         }
     }
 
@@ -142,6 +149,8 @@ impl WslBridge {
             conversation_id: Some(conversation_id),
             received_init: Arc::new(AtomicBool::new(false)),
             intentional_stop: Arc::new(AtomicBool::new(false)),
+            pending_since: Arc::new(Mutex::new(None)),
+            watchdog_generation: Arc::new(AtomicU64::new(0)),
         }
     }
 
@@ -442,6 +451,7 @@ impl WslBridge {
             let conv_id = self.conversation_id.clone();
             let received_init_clone = self.received_init.clone();
             let intentional_stop_clone = self.intentional_stop.clone();
+            let pending_since_clone = self.pending_since.clone();
             thread::spawn(move || {
                 handle_stdout(
                     stdout,
@@ -450,6 +460,7 @@ impl WslBridge {
                     conv_id,
                     received_init_clone,
                     intentional_stop_clone,
+                    pending_since_clone,
                 );
             });
         }
@@ -487,6 +498,48 @@ impl WslBridge {
             }
         });
 
+        // Reset the pending-since tracker for this new session so stale state from a previous
+        // session never triggers the mid-session watchdog immediately.
+        *self.pending_since.lock() = None;
+
+        // Mid-session watchdog: if a user message is sent but no Result arrives within 5 minutes,
+        // the Claude Code process is stuck. Kill it so the user gets a disconnect event and can
+        // reconnect. The generation counter ensures old watchdogs from previous sessions exit
+        // cleanly when `start()` is called again.
+        let generation = self.watchdog_generation.fetch_add(1, Ordering::SeqCst) + 1;
+        let process_mid_watchdog = self.process.clone();
+        let pending_since_watchdog = self.pending_since.clone();
+        let generation_watchdog = self.watchdog_generation.clone();
+        const STUCK_TIMEOUT: Duration = Duration::from_secs(5 * 60);
+        const POLL_INTERVAL: Duration = Duration::from_secs(30);
+        thread::spawn(move || {
+            loop {
+                thread::sleep(POLL_INTERVAL);
+                // Exit if a newer session has started.
+                if generation_watchdog.load(Ordering::SeqCst) != generation {
+                    break;
+                }
+                // Exit if the process has already been taken (killed or stopped).
+                if process_mid_watchdog.lock().is_none() {
+                    break;
+                }
+                let elapsed = (*pending_since_watchdog.lock()).map(|t| t.elapsed());
+                if let Some(elapsed) = elapsed {
+                    if elapsed >= STUCK_TIMEOUT {
+                        tracing::warn!(
+                            "Mid-session watchdog: no Result received in {:?}; killing stuck process",
+                            elapsed
+                        );
+                        if let Some(mut proc) = process_mid_watchdog.lock().take() {
+                            let _ = proc.kill();
+                            let _ = proc.wait();
+                        }
+                        break;
+                    }
+                }
+            }
+        });
+
         Ok(())
     }
 
@@ -523,6 +576,10 @@ impl WslBridge {
             .flush()
             .map_err(|e| format!("Failed to flush stdin: {}", e))?;
 
+        // Record the time this message was sent so the mid-session watchdog can detect
+        // if no Result ever arrives (i.e. the process is stuck).
+        *self.pending_since.lock() = Some(Instant::now());
+
         Ok(())
     }
 
@@ -762,15 +819,21 @@ fn handle_stdout(
     conversation_id: Option<String>,
     received_init: Arc<AtomicBool>,
     intentional_stop: Arc<AtomicBool>,
+    pending_since: Arc<Mutex<Option<Instant>>>,
 ) {
     let reader = BufReader::new(stdout);
 
     for line in reader.lines() {
         match line {
             Ok(line) if !line.is_empty() => {
-                if let Err(e) =
-                    process_json_line(&line, &app, &stats, &conversation_id, &received_init)
-                {
+                if let Err(e) = process_json_line(
+                    &line,
+                    &app,
+                    &stats,
+                    &conversation_id,
+                    &received_init,
+                    &pending_since,
+                ) {
                     tracing::error!("Error processing line: {}", e);
                 }
             }
@@ -1026,6 +1089,7 @@ fn process_json_line(
     stats: &Arc<RwLock<UsageStats>>,
     conversation_id: &Option<String>,
     received_init: &Arc<AtomicBool>,
+    pending_since: &Arc<Mutex<Option<Instant>>>,
 ) -> Result<(), String> {
     let message: ClaudeMessage = serde_json::from_str(line)
         .map_err(|e| format!("Failed to parse JSON: {} - Line: {}", e, line))?;
@@ -1412,6 +1476,10 @@ fn process_json_line(
                 permission_denials.as_ref().map(|d| d.len())
             );
 
+            // A Result means the turn is complete — clear pending_since so the mid-session
+            // watchdog knows the process is not stuck.
+            *pending_since.lock() = None;
+
             let state = if subtype == "success" {
                 CharacterState::Success
             } else {
@@ -2493,4 +2561,98 @@ mod tests {
             panic!("Expected ToolResult variant");
         }
     }
+
+    // Mid-session watchdog: pending_since lifecycle tests
+
+    #[test]
+    fn test_pending_since_starts_as_none() {
+        let bridge = WslBridge::new();
+        assert!(bridge.pending_since.lock().is_none());
+    }
+
+    #[test]
+    fn test_watchdog_generation_starts_at_zero() {
+        let bridge = WslBridge::new();
+        assert_eq!(bridge.watchdog_generation.load(Ordering::SeqCst), 0);
+    }
+
+    #[test]
+    fn test_pending_since_set_reflects_elapsed_time() {
+        let pending_since: Arc<Mutex<Option<Instant>>> = Arc::new(Mutex::new(None));
+
+        // Simulate send_message setting pending_since
+        *pending_since.lock() = Some(Instant::now());
+
+        // Should be Some and elapsed should be tiny (< 1 second)
+        let elapsed = (*pending_since.lock()).map(|t| t.elapsed());
+        assert!(elapsed.is_some());
+        assert!(elapsed.unwrap() < Duration::from_secs(1));
+    }
+
+    #[test]
+    fn test_pending_since_cleared_on_result_simulates_watchdog_safe() {
+        let pending_since: Arc<Mutex<Option<Instant>>> = Arc::new(Mutex::new(None));
+
+        // Simulate send_message
+        *pending_since.lock() = Some(Instant::now());
+        assert!(pending_since.lock().is_some());
+
+        // Simulate Result message arriving (as process_json_line does)
+        *pending_since.lock() = None;
+        assert!(pending_since.lock().is_none());
+
+        // Watchdog check: elapsed is None → no kill triggered
+        let elapsed = (*pending_since.lock()).map(|t| t.elapsed());
+        assert!(elapsed.is_none());
+    }
+
+    #[test]
+    fn test_watchdog_generation_increments_per_session() {
+        let bridge = WslBridge::new();
+        assert_eq!(bridge.watchdog_generation.load(Ordering::SeqCst), 0);
+
+        // Simulate what start() does: fetch_add(1) returns old value, +1 gives new generation
+        let gen1 = bridge.watchdog_generation.fetch_add(1, Ordering::SeqCst) + 1;
+        assert_eq!(gen1, 1);
+        assert_eq!(bridge.watchdog_generation.load(Ordering::SeqCst), 1);
+
+        let gen2 = bridge.watchdog_generation.fetch_add(1, Ordering::SeqCst) + 1;
+        assert_eq!(gen2, 2);
+        assert_eq!(bridge.watchdog_generation.load(Ordering::SeqCst), 2);
+    }
+
+    #[test]
+    fn test_watchdog_generation_mismatch_means_old_session() {
+        // Simulate: watchdog captured generation=1, but start() was called again → generation=2.
+        // The watchdog should detect this and exit without killing.
+        let generation_arc: Arc<AtomicU64> = Arc::new(AtomicU64::new(1));
+        let captured_generation: u64 = 1;
+
+        assert_eq!(generation_arc.load(Ordering::SeqCst), captured_generation, "same session");
+
+        // New start() call increments generation
+        generation_arc.fetch_add(1, Ordering::SeqCst);
+
+        assert_ne!(
+            generation_arc.load(Ordering::SeqCst),
+            captured_generation,
+            "old watchdog detects new session and should exit"
+        );
+    }
+
+    #[test]
+    fn test_stuck_timeout_threshold() {
+        // The timeout constant used in the mid-session watchdog is 5 minutes.
+        // This test documents and validates that threshold.
+        const STUCK_TIMEOUT: Duration = Duration::from_secs(5 * 60);
+        assert_eq!(STUCK_TIMEOUT, Duration::from_secs(300));
+
+        // A message sent 4m59s ago should NOT trigger the watchdog
+        let just_under = Duration::from_secs(299);
+        assert!(just_under < STUCK_TIMEOUT);
+
+        // A message sent 5m0s ago SHOULD trigger the watchdog
+        let exactly_at = Duration::from_secs(300);
+        assert!(exactly_at >= STUCK_TIMEOUT);
+    }
 }