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/PERIODIC_SAVE_QUICK_START.md

@@ -0,0 +1,236 @@
+# Periodic Context Save - Quick Start
+
+**Auto-save context every 5 minutes of active work**
+
+---
+
+## ✅ System Tested and Working
+
+The periodic context save system has been tested and is working correctly. It:
+- ✅ Detects Claude Code activity
+- ✅ Tracks active work time (not idle time)
+- ✅ Saves context to database every 5 minutes
+- ✅ Currently has 2 contexts saved
+
+---
+
+## Setup (One-Time)
+
+### Option 1: Automatic Setup (Recommended)
+
+Run this PowerShell command as Administrator:
+
+```powershell
+powershell -ExecutionPolicy Bypass -File D:\ClaudeTools\.claude\hooks\setup_periodic_save.ps1
+```
+
+This creates a Windows Task Scheduler task that runs every minute.
+
+### Option 2: Manual Setup
+
+1. Open **Task Scheduler** (taskschd.msc)
+2. Create Basic Task:
+   - **Name:** `ClaudeTools - Periodic Context Save`
+   - **Trigger:** Daily, repeat every 1 minute
+   - **Action:** Start a program
+     - Program: `python`
+     - Arguments: `D:\ClaudeTools\.claude\hooks\periodic_save_check.py`
+     - Start in: `D:\ClaudeTools`
+   - **Settings:**
+     - ✅ Allow task to run on batteries
+     - ✅ Start task if connection is not available
+     - ✅ Run task as soon as possible after missed start
+
+---
+
+## Verify It's Working
+
+### Check Status
+
+```bash
+# View recent logs
+tail -10 .claude/periodic-save.log
+
+# Check current state
+cat .claude/.periodic-save-state.json | python -m json.tool
+```
+
+**Expected output:**
+```json
+{
+  "active_seconds": 120,
+  "last_save": "2026-01-17T19:00:32+00:00",
+  "last_check": "2026-01-17T19:02:15+00:00"
+}
+```
+
+### Check Database
+
+```bash
+curl -s "http://172.16.3.30:8001/api/conversation-contexts?limit=5" \
+  -H "Authorization: Bearer YOUR_JWT_TOKEN" \
+  | python -m json.tool
+```
+
+Look for contexts with title starting with "Periodic Save -"
+
+---
+
+## How It Works
+
+```
+Every 1 minute:
+├─ Task Scheduler runs periodic_save_check.py
+├─ Script checks: Is Claude Code active?
+│  ├─ YES → Add 60s to timer
+│  └─ NO  → Don't add time (idle)
+├─ Check: Has timer reached 300s (5 min)?
+│  ├─ YES → Save context to DB, reset timer
+│  └─ NO  → Continue
+└─ Update state file
+```
+
+**Active time =** File changes + Claude running + Recent activity
+**Idle time =** No changes + Waiting for input + Permissions prompts
+
+---
+
+## What Gets Saved
+
+Every 5 minutes of active work:
+
+```json
+{
+  "context_type": "session_summary",
+  "title": "Periodic Save - 2026-01-17 12:00",
+  "dense_summary": "Auto-saved context after 5 minutes of active work...",
+  "relevance_score": 5.0,
+  "tags": ["auto-save", "periodic", "active-session"]
+}
+```
+
+---
+
+## Monitor Activity
+
+### View Logs in Real-Time
+
+```bash
+# Windows (PowerShell)
+Get-Content .claude\periodic-save.log -Tail 20 -Wait
+
+# Git Bash
+tail -f .claude/periodic-save.log
+```
+
+### Check Task Scheduler
+
+```powershell
+Get-ScheduledTask -TaskName "ClaudeTools - Periodic Context Save"
+```
+
+---
+
+## Troubleshooting
+
+### Not Saving Contexts
+
+**Check if task is running:**
+```powershell
+Get-ScheduledTask -TaskName "ClaudeTools - Periodic Context Save" | Get-ScheduledTaskInfo
+```
+
+**Check logs for errors:**
+```bash
+tail -20 .claude/periodic-save.log
+```
+
+**Common issues:**
+- JWT token expired (regenerate with `python create_jwt_token.py`)
+- Python not in PATH (add Python to system PATH)
+- API not accessible (check `curl http://172.16.3.30:8001/health`)
+
+### Activity Not Detected
+
+The script looks for:
+- Recent file modifications (within 2 minutes)
+- Claude/Node/Code processes running
+- Activity in project directories
+
+If it's not detecting activity, check:
+```bash
+# Is Python finding recent file changes?
+python -c "from pathlib import Path; import time; print([f.name for f in Path('.').rglob('*') if f.is_file() and f.stat().st_mtime > time.time()-120][:5])"
+```
+
+---
+
+## Configuration
+
+### Change Save Interval
+
+Edit `.claude/hooks/periodic_save_check.py`:
+
+```python
+SAVE_INTERVAL_SECONDS = 300  # Change to desired interval
+
+# Common values:
+# 300  = 5 minutes
+# 600  = 10 minutes
+# 900  = 15 minutes
+# 1800 = 30 minutes
+```
+
+### Change Check Frequency
+
+Modify Task Scheduler trigger to run every 30 seconds or 2 minutes instead of 1 minute.
+
+---
+
+## Uninstall
+
+```powershell
+# Remove Task Scheduler task
+Unregister-ScheduledTask -TaskName "ClaudeTools - Periodic Context Save" -Confirm:$false
+
+# Optional: Remove files
+Remove-Item .claude\hooks\periodic_save_check.py
+Remove-Item .claude\.periodic-save-state.json
+Remove-Item .claude\periodic-save.log
+```
+
+---
+
+## Integration
+
+Works alongside existing hooks:
+
+| Hook | When | What It Saves |
+|------|------|---------------|
+| user-prompt-submit | Before each message | Recalls context |
+| task-complete | After task done | Detailed summary |
+| **periodic_save_check** | **Every 5 min active** | **Quick checkpoint** |
+
+**Result:** Never lose more than 5 minutes of context!
+
+---
+
+## Current Status
+
+✅ **System is installed and working**
+✅ **2 contexts already saved to database**
+✅ **Ready to set up Task Scheduler for automatic saves**
+
+---
+
+**Next Step:** Run the PowerShell setup script to enable automatic periodic saves:
+
+```powershell
+powershell -ExecutionPolicy Bypass -File D:\ClaudeTools\.claude\hooks\setup_periodic_save.ps1
+```
+
+---
+
+**Created:** 2026-01-17
+**Tested:** ✅ Working
+**Database:** 172.16.3.30:3306/claudetools