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/stores/snippets.test.ts

@@ -285,6 +285,73 @@ describe("snippetsStore", () => {
       expect(get(snippetsStore.selectedCategory)).toBeNull();
     });
   });
+
+  describe("filteredSnippets", () => {
+    it("returns all snippets when no category selected", async () => {
+      const mockSnippets: Snippet[] = [
+        {
+          id: "snippet-1",
+          name: "Git Status",
+          content: "git status",
+          category: "Git",
+          is_default: false,
+          created_at: "2024-01-01T00:00:00Z",
+          updated_at: "2024-01-01T00:00:00Z",
+        },
+        {
+          id: "snippet-2",
+          name: "Docker PS",
+          content: "docker ps",
+          category: "Docker",
+          is_default: false,
+          created_at: "2024-01-01T00:00:00Z",
+          updated_at: "2024-01-01T00:00:00Z",
+        },
+      ];
+
+      setMockInvokeResult("list_snippets", mockSnippets);
+      setMockInvokeResult("get_snippet_categories", ["Git", "Docker"]);
+
+      await snippetsStore.loadSnippets();
+      snippetsStore.setSelectedCategory(null);
+
+      const filtered = get(snippetsStore.filteredSnippets);
+      expect(filtered).toHaveLength(2);
+    });
+
+    it("filters snippets by selected category", async () => {
+      const mockSnippets: Snippet[] = [
+        {
+          id: "snippet-1",
+          name: "Git Status",
+          content: "git status",
+          category: "Git",
+          is_default: false,
+          created_at: "2024-01-01T00:00:00Z",
+          updated_at: "2024-01-01T00:00:00Z",
+        },
+        {
+          id: "snippet-2",
+          name: "Docker PS",
+          content: "docker ps",
+          category: "Docker",
+          is_default: false,
+          created_at: "2024-01-01T00:00:00Z",
+          updated_at: "2024-01-01T00:00:00Z",
+        },
+      ];
+
+      setMockInvokeResult("list_snippets", mockSnippets);
+      setMockInvokeResult("get_snippet_categories", ["Git", "Docker"]);
+
+      await snippetsStore.loadSnippets();
+      snippetsStore.setSelectedCategory("Git");
+
+      const filtered = get(snippetsStore.filteredSnippets);
+      expect(filtered).toHaveLength(1);
+      expect(filtered[0].category).toBe("Git");
+    });
+  });
 });
 
 describe("snippet ID generation", () => {