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-tauri/Cargo.lock

@@ -1658,6 +1658,8 @@ dependencies = [
  "tauri-plugin-store",
  "tempfile",
  "tokio",
+ "tracing",
+ "tracing-subscriber",
  "uuid 1.19.0",
  "windows 0.62.2",
 ]
@@ -2245,6 +2247,15 @@ dependencies = [
  "syn 2.0.114",
 ]
 
+[[package]]
+name = "matchers"
+version = "0.2.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d1525a2a28c7f4fa0fc98bb91ae755d1e2d1505079e05539e35bc876b5d65ae9"
+dependencies = [
+ "regex-automata",
+]
+
 [[package]]
 name = "matches"
 version = "0.1.10"
@@ -2401,6 +2412,15 @@ dependencies = [
  "zbus",
 ]
 
+[[package]]
+name = "nu-ansi-term"
+version = "0.50.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "7957b9740744892f114936ab4a57b3f487491bbeafaf8083688b16841a4240e5"
+dependencies = [
+ "windows-sys 0.61.2",
+]
+
 [[package]]
 name = "num-conv"
 version = "0.1.0"
@@ -3879,6 +3899,15 @@ dependencies = [
  "digest",
 ]
 
+[[package]]
+name = "sharded-slab"
+version = "0.1.7"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "f40ca3c46823713e0d4209592e8d6e826aa57e928f09752619fc696c499637f6"
+dependencies = [
+ "lazy_static",
+]
+
 [[package]]
 name = "shared_child"
 version = "1.1.1"
@@ -4695,6 +4724,15 @@ dependencies = [
  "syn 2.0.114",
 ]
 
+[[package]]
+name = "thread_local"
+version = "1.1.9"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "f60246a4944f24f6e018aa17cdeffb7818b76356965d03b07d6a9886e8962185"
+dependencies = [
+ "cfg-if",
+]
+
 [[package]]
 name = "tiff"
 version = "0.10.3"
@@ -4986,6 +5024,36 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "db97caf9d906fbde555dd62fa95ddba9eecfd14cb388e4f491a66d74cd5fb79a"
 dependencies = [
  "once_cell",
+ "valuable",
+]
+
+[[package]]
+name = "tracing-log"
+version = "0.2.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ee855f1f400bd0e5c02d150ae5de3840039a3f54b025156404e34c23c03f47c3"
+dependencies = [
+ "log",
+ "once_cell",
+ "tracing-core",
+]
+
+[[package]]
+name = "tracing-subscriber"
+version = "0.3.22"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "2f30143827ddab0d256fd843b7a66d164e9f271cfa0dde49142c5ca0ca291f1e"
+dependencies = [
+ "matchers",
+ "nu-ansi-term",
+ "once_cell",
+ "regex-automata",
+ "sharded-slab",
+ "smallvec",
+ "thread_local",
+ "tracing",
+ "tracing-core",
+ "tracing-log",
 ]
 
 [[package]]
@@ -5167,6 +5235,12 @@ dependencies = [
  "wasm-bindgen",
 ]
 
+[[package]]
+name = "valuable"
+version = "0.1.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ba73ea9cf16a25df0c8caa16c51acb937d5712a8429db78a3ee29d5dcacd3a65"
+
 [[package]]
 name = "version-compare"
 version = "0.2.1"