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>

check-all.sh

@@ -1,5 +1,9 @@
 #!/bin/bash
 
+# Source nvm to get access to pnpm
+export NVM_DIR="$HOME/.nvm"
+[ -s "$NVM_DIR/nvm.sh" ] && \. "$NVM_DIR/nvm.sh"
+
 # Colors for output
 RED='\033[0;31m'
 GREEN='\033[0;32m'
@@ -32,11 +36,11 @@ echo -e "${YELLOW}🔍 Running all checks for Hikari Desktop...${NC}"
 run_check "Frontend lint" "pnpm lint" || failed=1
 run_check "Frontend format check" "pnpm format:check" || failed=1
 run_check "Frontend type check" "pnpm check" || failed=1
-run_check "Frontend tests" "pnpm test" || failed=1
+run_check "Frontend tests with coverage" "pnpm test:coverage" || failed=1
 
 # Backend checks
-run_check "Backend clippy (strict)" "cd src-tauri && cargo clippy --all-targets --all-features -- -D warnings" || failed=1
-run_check "Backend tests" "cargo test" || failed=1
+run_check "Backend clippy (strict)" "(cd src-tauri && cargo clippy --all-targets --all-features -- -D warnings)" || failed=1
+run_check "Backend tests with coverage" "(cd src-tauri && cargo llvm-cov --fail-under-lines 50)" || failed=1
 
 # Summary
 echo -e "\n${YELLOW}========================================${NC}"