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/lib/stores/claude.ts

@@ -41,6 +41,7 @@ export const claudeStore = {
   setWorkingDirectory: conversationsStore.setWorkingDirectory,
   setWorkingDirectoryForConversation: conversationsStore.setWorkingDirectoryForConversation,
   setProcessing: conversationsStore.setProcessing,
+  setProcessingForConversation: conversationsStore.setProcessingForConversation,
   addLine: conversationsStore.addLine,
   addLineToConversation: conversationsStore.addLineToConversation,
   updateLine: conversationsStore.updateLine,

src/lib/stores/conversations.test.ts

@@ -561,3 +561,99 @@ describe("draft text persistence", () => {
     expect(conversation.draftText).toBe("");
   });
 });
+
+describe("isProcessing state management", () => {
+  it("starts as false by default", () => {
+    const conversation = { id: "conv-1", isProcessing: false };
+    expect(conversation.isProcessing).toBe(false);
+  });
+
+  it("setProcessingForConversation sets processing true for the target conversation", () => {
+    const conversations = new Map([
+      ["conv-1", { isProcessing: false, lastActivityAt: new Date(0) }],
+      ["conv-2", { isProcessing: false, lastActivityAt: new Date(0) }],
+    ]);
+
+    const setProcessingForConversation = (conversationId: string, processing: boolean) => {
+      const conv = conversations.get(conversationId);
+      if (conv) {
+        conv.isProcessing = processing;
+        conv.lastActivityAt = new Date();
+      }
+    };
+
+    setProcessingForConversation("conv-1", true);
+
+    expect(conversations.get("conv-1")?.isProcessing).toBe(true);
+    expect(conversations.get("conv-2")?.isProcessing).toBe(false);
+  });
+
+  it("setProcessingForConversation resets processing to false", () => {
+    const conversations = new Map([
+      ["conv-1", { isProcessing: true, lastActivityAt: new Date(0) }],
+    ]);
+
+    const setProcessingForConversation = (conversationId: string, processing: boolean) => {
+      const conv = conversations.get(conversationId);
+      if (conv) {
+        conv.isProcessing = processing;
+        conv.lastActivityAt = new Date();
+      }
+    };
+
+    setProcessingForConversation("conv-1", false);
+
+    expect(conversations.get("conv-1")?.isProcessing).toBe(false);
+  });
+
+  it("setProcessingForConversation does nothing for unknown conversation", () => {
+    const conversations = new Map([
+      ["conv-1", { isProcessing: false, lastActivityAt: new Date(0) }],
+    ]);
+
+    const setProcessingForConversation = (conversationId: string, processing: boolean) => {
+      const conv = conversations.get(conversationId);
+      if (conv) {
+        conv.isProcessing = processing;
+        conv.lastActivityAt = new Date();
+      }
+    };
+
+    setProcessingForConversation("unknown", true);
+
+    expect(conversations.get("conv-1")?.isProcessing).toBe(false);
+  });
+
+  it("isProcessing is cleared when idle state arrives", () => {
+    const conversation = { isProcessing: true, characterState: "thinking" };
+
+    const terminalStates = ["idle", "success", "error"];
+    const handleStateChange = (state: string) => {
+      conversation.characterState = state;
+      if (terminalStates.includes(state)) {
+        conversation.isProcessing = false;
+      }
+    };
+
+    handleStateChange("idle");
+
+    expect(conversation.isProcessing).toBe(false);
+  });
+
+  it("isProcessing stays true during non-terminal states", () => {
+    const conversation = { isProcessing: true, characterState: "thinking" };
+
+    const terminalStates = ["idle", "success", "error"];
+    const handleStateChange = (state: string) => {
+      conversation.characterState = state;
+      if (terminalStates.includes(state)) {
+        conversation.isProcessing = false;
+      }
+    };
+
+    for (const state of ["thinking", "typing", "coding", "searching", "mcp"]) {
+      handleStateChange(state);
+      expect(conversation.isProcessing).toBe(true);
+    }
+  });
+});

src/lib/stores/conversations.ts

@@ -560,6 +560,17 @@ function createConversationsStore() {
       });
     },
 
+    setProcessingForConversation: (conversationId: string, processing: boolean) => {
+      conversations.update((convs) => {
+        const conv = convs.get(conversationId);
+        if (conv) {
+          conv.isProcessing = processing;
+          conv.lastActivityAt = new Date();
+        }
+        return convs;
+      });
+    },
+
     addLine: (
       type: TerminalLine["type"],
       content: string,