feat: Major directory reorganization and cleanup

Reorganized project structure for better maintainability and reduced
disk usage by 95.9% (11 GB -> 451 MB).

Directory Reorganization (85% reduction in root files):
- Created docs/ with subdirectories (deployment, testing, database, etc.)
- Created infrastructure/vpn-configs/ for VPN scripts
- Moved 90+ files from root to organized locations
- Archived obsolete documentation (context system, offline mode, zombie debugging)
- Moved all test files to tests/ directory
- Root directory: 119 files -> 18 files

Disk Cleanup (10.55 GB recovered):
- Deleted Rust build artifacts: 9.6 GB (target/ directories)
- Deleted Python virtual environments: 161 MB (venv/ directories)
- Deleted Python cache: 50 KB (__pycache__/)

New Structure:
- docs/ - All documentation organized by category
- docs/archives/ - Obsolete but preserved documentation
- infrastructure/ - VPN configs and SSH setup
- tests/ - All test files consolidated
- logs/ - Ready for future logs

Benefits:
- Cleaner root directory (18 vs 119 files)
- Logical organization of documentation
- 95.9% disk space reduction
- Faster navigation and discovery
- Better portability (build artifacts excluded)

Build artifacts can be regenerated:
- Rust: cargo build --release (5-15 min per project)
- Python: pip install -r requirements.txt (2-3 min)

Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>

docs/archives/offline-mode-removed/INVISIBLE_PERIODIC_SAVE_SUMMARY.md

@@ -0,0 +1,219 @@
+# Periodic Save Task - Invisible Mode Setup
+
+## Problem Solved
+The `periodic_save_check.py` Task Scheduler task was showing a flashing console window every minute. This has been fixed by configuring the task to run completely invisibly.
+
+---
+
+## What Changed
+
+### 1. Updated Setup Script
+**File:** `D:\ClaudeTools\.claude\hooks\setup_periodic_save.ps1`
+
+**Changes:**
+- Uses `pythonw.exe` instead of `python.exe` (no console window)
+- Added `-Hidden` flag to task settings
+- Changed LogonType from `Interactive` to `S4U` (Service-For-User = background)
+- Added verification instructions in output
+
+### 2. Created Update Script
+**File:** `D:\ClaudeTools\.claude\hooks\update_to_invisible.ps1`
+
+**Purpose:**
+- Quick one-command update for existing tasks
+- Preserves existing triggers and settings
+- Validates pythonw.exe exists
+- Shows verification output
+
+### 3. Created Documentation
+**File:** `D:\ClaudeTools\.claude\PERIODIC_SAVE_INVISIBLE_SETUP.md`
+
+**Contents:**
+- Automatic setup instructions
+- Manual update procedures (PowerShell and GUI)
+- Verification steps
+- Troubleshooting guide
+
+---
+
+## How to Fix Your Current Task
+
+### Option 1: Automatic (Recommended)
+
+Run the update script:
+
+```powershell
+# From PowerShell in D:\ClaudeTools
+.\.claude\hooks\update_to_invisible.ps1
+```
+
+This will:
+- Find pythonw.exe automatically
+- Update the task to use pythonw.exe
+- Set the task to run hidden
+- Verify all settings are correct
+
+### Option 2: Recreate Task
+
+Re-run the setup script (removes old task and creates new one):
+
+```powershell
+# From PowerShell in D:\ClaudeTools
+.\.claude\hooks\setup_periodic_save.ps1
+```
+
+### Option 3: Manual (GUI)
+
+1. Open Task Scheduler (Win + R → `taskschd.msc`)
+2. Find "ClaudeTools - Periodic Context Save"
+3. Right-click → Properties
+4. **Actions tab:** Change `python.exe` to `pythonw.exe`
+5. **General tab:** Check "Hidden" checkbox
+6. Click OK
+
+---
+
+## Verification
+
+After updating, verify the task is configured correctly:
+
+```powershell
+# Quick verification
+Get-ScheduledTask -TaskName "ClaudeTools - Periodic Context Save" |
+    Select-Object -ExpandProperty Actions |
+    Select-Object Execute
+
+# Should show: ...pythonw.exe (NOT python.exe)
+
+# Check hidden setting
+Get-ScheduledTask -TaskName "ClaudeTools - Periodic Context Save" |
+    Select-Object -ExpandProperty Settings |
+    Select-Object Hidden
+
+# Should show: Hidden: True
+```
+
+---
+
+## Technical Details
+
+### pythonw.exe vs python.exe
+
+| Executable | Console Window | Use Case |
+|------------|---------------|----------|
+| `python.exe` | Shows console | Interactive scripts, debugging |
+| `pythonw.exe` | No console | Background tasks, GUI apps |
+
+### Task Scheduler Settings
+
+| Setting | Old Value | New Value | Purpose |
+|---------|-----------|-----------|---------|
+| Executable | python.exe | pythonw.exe | No console window |
+| Hidden | False | True | Hide from task list |
+| LogonType | Interactive | S4U | Run in background |
+
+### What is S4U (Service-For-User)?
+
+- Runs tasks in background session
+- No interactive window
+- Doesn't require user to be logged in
+- Ideal for background automation
+
+---
+
+## Files Modified/Created
+
+### Modified
+- `D:\ClaudeTools\.claude\hooks\setup_periodic_save.ps1`
+  - Lines 9-18: Auto-detect pythonw.exe path
+  - Line 29: Use pythonw.exe instead of python.exe
+  - Line 43: Added `-Hidden` flag
+  - Line 46: Changed LogonType to S4U
+  - Lines 59-64: Updated output messages
+
+### Created
+- `D:\ClaudeTools\.claude\hooks\update_to_invisible.ps1`
+  - Quick update script for existing tasks
+
+- `D:\ClaudeTools\.claude\PERIODIC_SAVE_INVISIBLE_SETUP.md`
+  - Complete setup and troubleshooting guide
+
+- `D:\ClaudeTools\INVISIBLE_PERIODIC_SAVE_SUMMARY.md`
+  - This file - quick reference summary
+
+---
+
+## Testing
+
+After updating, the task will run every minute but you should see:
+- ✓ No console window flashing
+- ✓ No visible task execution
+- ✓ Logs still being written to `D:\ClaudeTools\.claude\periodic-save.log`
+
+Check logs to verify it's working:
+
+```powershell
+Get-Content D:\ClaudeTools\.claude\periodic-save.log -Tail 20
+```
+
+You should see log entries appearing every minute (when Claude is active) without any visible window.
+
+---
+
+## Troubleshooting
+
+### Still seeing console window?
+
+**Check executable:**
+```powershell
+Get-ScheduledTask -TaskName "ClaudeTools - Periodic Context Save" |
+    Select-Object -ExpandProperty Actions
+```
+- If shows `python.exe` - update didn't work, try manual update
+- If shows `pythonw.exe` - should be invisible (check hidden setting)
+
+**Check hidden setting:**
+```powershell
+Get-ScheduledTask -TaskName "ClaudeTools - Periodic Context Save" |
+    Select-Object -ExpandProperty Settings |
+    Select-Object Hidden
+```
+- Should show `Hidden: True`
+- If False, run update script again
+
+**Check LogonType:**
+```powershell
+Get-ScheduledTask -TaskName "ClaudeTools - Periodic Context Save" |
+    Select-Object -ExpandProperty Principal
+```
+- Should show `LogonType: S4U`
+- If Interactive, run update script again
+
+### pythonw.exe not found?
+
+```powershell
+# Check Python installation
+Get-Command python | Select-Object -ExpandProperty Source
+
+# Check if pythonw.exe exists in same directory
+$PythonPath = (Get-Command python).Source
+$PythonDir = Split-Path $PythonPath -Parent
+Test-Path (Join-Path $PythonDir "pythonw.exe")
+```
+
+If False, reinstall Python. pythonw.exe should always come with Python on Windows.
+
+---
+
+## Current Status
+
+**Task Name:** ClaudeTools - Periodic Context Save
+**Frequency:** Every 1 minute
+**Action:** Check activity, save context every 5 minutes of active work
+**Visibility:** Hidden (no console window)
+**Logs:** `D:\ClaudeTools\.claude\periodic-save.log`
+
+---
+
+**Last Updated:** 2026-01-17
+**Updated Files:** 1 modified, 3 created