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/zombie-process-debugging/FIX_FLASHING_WINDOW.md

@@ -0,0 +1,60 @@
+# FIX: Stop Console Window from Flashing
+
+## Problem
+The periodic save task shows a flashing console window every minute.
+
+## Solution (Pick One)
+
+### Option 1: Quick Update (Recommended)
+```powershell
+# Run this in PowerShell
+.\.claude\hooks\update_to_invisible.ps1
+```
+
+### Option 2: Recreate Task
+```powershell
+# Run this in PowerShell
+.\.claude\hooks\setup_periodic_save.ps1
+```
+
+### Option 3: Manual Fix (Task Scheduler GUI)
+1. Open Task Scheduler (Win+R → `taskschd.msc`)
+2. Find "ClaudeTools - Periodic Context Save"
+3. Right-click → Properties
+4. **Actions tab:** Change Program/script from `python.exe` to `pythonw.exe`
+5. **General tab:** Check "Hidden" checkbox
+6. Click OK
+
+---
+
+## Verify It Worked
+
+```powershell
+# Check the executable
+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
+```
+
+---
+
+## What This Does
+
+- Changes from `python.exe` → `pythonw.exe` (no console window)
+- Sets task to run hidden
+- Changes to background mode (S4U LogonType)
+
+**Result:** Task runs invisibly - no more flashing windows!
+
+---
+
+**See:** `INVISIBLE_PERIODIC_SAVE_SUMMARY.md` for complete details