fix: critical permission modal and config issues (#127)

## Summary

This PR resolves several critical bugs that were blocking the permission modal and causing config loss:

- **Permission modal not appearing** - Fixed z-index issues and runtime errors
- **Config store race condition** - Resolved critical race condition causing settings to be lost
- **Excessive logging** - Removed redundant fmt layer that was writing to hidden stdout
- **System tool prompts** - Prevented unnecessary permission prompts for built-in tools
- **Permission batching** - Added support for parallel permission requests
- **ExitPlanMode tool** - Fixed ExitPlanMode tool not functioning correctly

## Changes Made

### Permission Modal Fixes
- Updated z-index to proper value (9999) to ensure modal appears above all other UI elements
- Fixed runtime errors that were preventing modal from rendering
- Resolved issues with permission grants not being properly applied

### Config Store Race Condition
- Fixed critical race condition where multiple rapid config updates would result in lost settings
- Ensured config writes are properly sequenced to prevent data loss
- Added proper synchronisation for config store operations

### Logging Cleanup
- Removed redundant fmt formatting layer that was outputting to hidden stdout
- Cleaned up excessive debug logging added during troubleshooting
- Removed temporary debugging documentation files

### UX Improvements
- Added close confirmation modal with minimise to tray option
- Implemented batching for parallel permission requests
- Added debug console for viewing frontend and backend logs

### ExitPlanMode Fix
- Fixed ExitPlanMode tool not functioning correctly, ensuring proper transitions out of plan mode

## Issues Resolved

Closes #112 - Permission flow now properly handles multiple tool requests
Closes #113 - ExitPlanMode tool now functions correctly
Closes #126 - Debug console feature added (partial - basic implementation complete)

## Test Plan

- [x] Permission modal appears and functions correctly
- [x] Config settings persist across app restarts
- [x] No excessive logging in production builds
- [x] System tools don't trigger permission prompts
- [x] Parallel permission requests are properly batched
- [x] Debug console displays frontend and backend logs
- [x] ExitPlanMode properly exits plan mode

---
✨ This PR was created with help from Hikari~ 🌸

Co-authored-by: Naomi Carrigan <commits@nhcarrigan.com>
Reviewed-on: #127
Co-authored-by: Hikari <hikari@nhcarrigan.com>
Co-committed-by: Hikari <hikari@nhcarrigan.com>

src/lib/utils/stateMapper.test.ts

@@ -135,6 +135,151 @@ describe("stateMapper", () => {
       };
       expect(mapMessageToState(message)).toBeNull();
     });
+
+    it("returns typing for unknown tool", () => {
+      const message: ClaudeStreamMessage = {
+        type: "assistant",
+        message: {
+          content: [
+            {
+              type: "tool_use",
+              id: "tool-1",
+              name: "SomeUnknownTool",
+              input: {},
+            },
+          ],
+          model: "claude-3",
+          stop_reason: "tool_use",
+        },
+      };
+      expect(mapMessageToState(message)).toBe("typing");
+    });
+
+    it("returns thinking for thinking content block", () => {
+      const message: ClaudeStreamMessage = {
+        type: "assistant",
+        message: {
+          content: [{ type: "thinking", thinking: "Analyzing the problem..." }],
+          model: "claude-3",
+          stop_reason: "end_turn",
+        },
+      };
+      expect(mapMessageToState(message)).toBe("thinking");
+    });
+
+    it("returns null for assistant message with no recognizable content", () => {
+      const message: ClaudeStreamMessage = {
+        type: "assistant",
+        message: {
+          content: [],
+          model: "claude-3",
+          stop_reason: "end_turn",
+        },
+      };
+      expect(mapMessageToState(message)).toBeNull();
+    });
+
+    it("returns thinking for thinking_delta stream event", () => {
+      const message: ClaudeStreamMessage = {
+        type: "stream_event",
+        event: {
+          type: "content_block_delta",
+          index: 0,
+          delta: {
+            type: "thinking_delta",
+            thinking: "Thinking...",
+          },
+        },
+      };
+      expect(mapMessageToState(message)).toBe("thinking");
+    });
+
+    it("returns typing for text_delta stream event", () => {
+      const message: ClaudeStreamMessage = {
+        type: "stream_event",
+        event: {
+          type: "content_block_delta",
+          index: 0,
+          delta: {
+            type: "text_delta",
+            text: "Hello",
+          },
+        },
+      };
+      expect(mapMessageToState(message)).toBe("typing");
+    });
+
+    it("returns thinking for thinking content_block_start", () => {
+      const message: ClaudeStreamMessage = {
+        type: "stream_event",
+        event: {
+          type: "content_block_start",
+          index: 0,
+          content_block: {
+            type: "thinking",
+            thinking: "",
+          },
+        },
+      };
+      expect(mapMessageToState(message)).toBe("thinking");
+    });
+
+    it("returns typing for text content_block_start", () => {
+      const message: ClaudeStreamMessage = {
+        type: "stream_event",
+        event: {
+          type: "content_block_start",
+          index: 0,
+          content_block: {
+            type: "text",
+            text: "",
+          },
+        },
+      };
+      expect(mapMessageToState(message)).toBe("typing");
+    });
+
+    it("returns correct state for tool_use content_block_start", () => {
+      const message: ClaudeStreamMessage = {
+        type: "stream_event",
+        event: {
+          type: "content_block_start",
+          index: 0,
+          content_block: {
+            type: "tool_use",
+            id: "tool-1",
+            name: "Read",
+            input: {},
+          },
+        },
+      };
+      expect(mapMessageToState(message)).toBe("searching");
+    });
+
+    it("returns null for stream_event with unrecognized type", () => {
+      const message: ClaudeStreamMessage = {
+        type: "stream_event",
+        event: {
+          type: "message_start",
+        },
+      };
+      expect(mapMessageToState(message)).toBeNull();
+    });
+
+    it("returns null for result with unknown subtype", () => {
+      const message = {
+        type: "result",
+        subtype: "unknown_type",
+      } as unknown as ClaudeStreamMessage;
+      expect(mapMessageToState(message)).toBeNull();
+    });
+
+    it("returns null for unknown message type", () => {
+      const message = {
+        type: "unknown_type",
+      } as unknown as ClaudeStreamMessage;
+      expect(mapMessageToState(message)).toBeNull();
+    });
   });
 
   describe("extractTextFromMessage", () => {
@@ -192,6 +337,36 @@ describe("stateMapper", () => {
       };
       expect(extractTextFromMessage(message)).toBe("Completed successfully");
     });
+
+    it("returns null for result without result field", () => {
+      const message: ClaudeStreamMessage = {
+        type: "result",
+        subtype: "success",
+      };
+      expect(extractTextFromMessage(message)).toBeNull();
+    });
+
+    it("returns null for stream_event without delta text", () => {
+      const message: ClaudeStreamMessage = {
+        type: "stream_event",
+        event: {
+          type: "content_block_start",
+          index: 0,
+          content_block: {
+            type: "text",
+            text: "",
+          },
+        },
+      };
+      expect(extractTextFromMessage(message)).toBeNull();
+    });
+
+    it("returns null for unknown message type", () => {
+      const message = {
+        type: "unknown",
+      } as unknown as ClaudeStreamMessage;
+      expect(extractTextFromMessage(message)).toBeNull();
+    });
   });
 
   describe("extractToolInfo", () => {