docs: remove stale run_autobot.sh references (#2468)

.claude/agents/frontend-engineer-agent.md

@@ -19,7 +19,7 @@ You are a Senior Frontend Engineer specializing in the AutoBot Vue 3 application
 - **NO** local development servers (`localhost:5173`)
 - **NO** multiple frontend instances permitted
 - **FORBIDDEN COMMANDS**: `npm run dev`, `yarn dev`, `vite dev` on main machine
-- **FRONTEND STARTS ONLY**: via `run_autobot.sh` script which manages VM
+- **FRONTEND STARTS ONLY**: via systemd services on the Frontend VM (.21), managed by Ansible
 
 **🚫 REMOTE HOST DEVELOPMENT RULES:**
 - **NEVER edit code directly on remote hosts** (172.16.168.21-25)
@@ -140,4 +140,3 @@ When developing components, always consider the multi-modal AI context, ensure s
 - Local-only development workflow
 - Repository cleanliness standards
 - VM sync procedures and SSH requirements
-

autobot-infrastructure/shared/analysis/ai-ml/llm_model_investigation_summary.md

@@ -163,7 +163,7 @@ ollama pull codellama:7b-instruct
 python scripts/ai-ml/model_references_corrector.py
 
 # 3. Test system functionality
-bash run_autobot.sh --dev --no-build
+sudo systemctl start autobot-backend
 
 # 4. Run full optimization (optional, but recommended)
 python scripts/ai-ml/optimize_llm_models.py

autobot-infrastructure/shared/analysis/chat_refactoring_plan.md

@@ -57,7 +57,7 @@ ROUTER_MAPPINGS = [
 #### Step 1.3: Test Immediate Resolution
 ```bash
 # Restart backend and verify single router active
-bash run_autobot.sh --dev --no-build
+sudo systemctl restart autobot-backend
 
 # Test key endpoints:
 curl http://localhost:8001/api/health
@@ -390,7 +390,7 @@ cp backend/fast_app_factory_fix.py.backup backend/fast_app_factory_fix.py
 cp autobot-vue/src/services/api.ts.backup autobot-vue/src/services/api.ts
 cp autobot-vue/src/utils/ApiClient.ts.backup autobot-vue/src/utils/ApiClient.ts
 # Restart services
-bash run_autobot.sh --dev --rebuild
+sudo systemctl restart autobot-backend
 ```
 
 ## Success Metrics

autobot-infrastructure/shared/scripts/README.md

@@ -5,7 +5,7 @@
 ```
 scripts/
 ├── analysis/         # Test scripts and analysis tools (moved from root)
-├── archive/          # Obsolete startup scripts (replaced by run_autobot.sh)
+├── archive/          # Obsolete startup scripts (deprecated, see SERVICE_MANAGEMENT.md)
 ├── cache/            # Cache management utilities
 ├── native-vm/        # Native VM deployment scripts
 ├── network/          # Network configuration and testing
@@ -22,13 +22,14 @@ scripts/
 
 ## Main Scripts (Root Directory)
 
-### Essential Scripts (ONLY 2 FILES)
-- **`run_autobot.sh`** - Unified startup script (combines all previous run scripts)
+### Essential Scripts
 - **`setup.sh`** - Unified setup script (handles all setup tasks)
+- **`scripts/start-services.sh`** - CLI service wrapper (start/stop/restart)
 
 ## Script Categories
 
-### Archive (Obsolete - Use run_autobot.sh instead)
+### Archive (Obsolete - Do not use)
+- `run_autobot.sh` - Deprecated (Issue #863), moved to `legacy/`
 - `run_agent.sh` - Old Docker-based startup
 - `run_agent_unified.sh` - Old unified startup
 - `run_agent_native.sh` - Old native VM startup
@@ -67,16 +68,16 @@ scripts/
 
 ## Usage Examples
 
-### Using the Unified Script (Recommended)
+### Starting Services (Recommended)
 ```bash
-# Standard native VM startup
-./run_autobot.sh
+# Production (systemd)
+sudo systemctl start autobot-backend
 
-# Development mode
-./run_autobot.sh --dev
+# CLI wrapper
+scripts/start-services.sh start
 
-# With specific options
-./run_autobot.sh --dev --no-browser --rebuild
+# Docker
+docker compose up -d
 ```
 
 ### Setup Commands
@@ -119,10 +120,12 @@ scripts/
 
 ## Migration Notes
 
-All old startup scripts have been consolidated into `run_autobot.sh`.
-If you were using:
-- `run_agent.sh --dev` → Now use `run_autobot.sh --dev`
-- `run_agent_native.sh` → Now use `run_autobot.sh` (native is default)
-- `run-docker-desktop.sh` → Now use `run_autobot.sh --docker`
+All old startup scripts (including `run_autobot.sh`) have been deprecated.
+Use the current methods:
+- **Production:** `systemctl start autobot-backend`
+- **CLI wrapper:** `scripts/start-services.sh start`
+- **Docker:** `docker compose up -d`
+
+See [`docs/developer/SERVICE_MANAGEMENT.md`](../../docs/developer/SERVICE_MANAGEMENT.md) for full details.
 
 The old scripts are preserved in `scripts/archive/` for reference but should not be used.

autobot-infrastructure/shared/scripts/security/ssh-hardening/README.md

@@ -112,7 +112,7 @@ This directory contains scripts to fix the critical SSH man-in-the-middle vulner
 - 50+ shell scripts in `scripts/` directory
 - Python modules with subprocess SSH calls
 - Ansible configuration files
-- Main system scripts (run_autobot.sh, etc.)
+- Main system scripts (now managed via systemd; `run_autobot.sh` deprecated)
 
 **Output**:
 - Backup directory: `backups/ssh-remediation-<timestamp>/`
@@ -225,7 +225,7 @@ This directory contains scripts to fix the critical SSH man-in-the-middle vulner
 9. **Full System Test**:
    ```bash
    # Start AutoBot with new SSH security
-   bash run_autobot.sh --dev
+   sudo systemctl start autobot-backend
    ```
 
 ### Phase 4: MITM Detection Verification (Optional)

autobot-infrastructure/shared/tests/performance/PERFORMANCE_BASELINE_SUMMARY.md

@@ -116,7 +116,7 @@ Established comprehensive performance baseline and validation framework for Auto
 cd /home/kali/Desktop/AutoBot
 
 # Ensure backend is running
-bash run_autobot.sh --dev
+sudo systemctl start autobot-backend
 
 # Execute baseline tests
 python tests/performance/test_async_baseline.py

autobot-infrastructure/shared/tests/performance/README_ASYNC_VALIDATION.md

@@ -178,7 +178,7 @@ comparison_report_YYYYMMDD.json      # Before/after analysis
 ### Prerequisites
 ```bash
 # Ensure AutoBot backend is running
-bash run_autobot.sh --dev
+sudo systemctl start autobot-backend
 
 # Install test dependencies (should already be installed)
 pip install aiohttp redis[asyncio] aiofiles

autobot-infrastructure/shared/tests/performance/run_baseline.sh

@@ -41,7 +41,7 @@ if ! curl -s -f "${BACKEND_URL}/api/health" > /dev/null 2>&1; then
     echo ""
     echo "Please start AutoBot first:"
     echo "  cd ${PROJECT_ROOT}"
-    echo "  bash run_autobot.sh --dev"
+    echo "  systemctl start autobot-backend  # or: scripts/start-services.sh start"
     echo ""
     exit 1
 fi

autobot-slm-backend/ansible/ROLE_STRUCTURE_README.md

@@ -382,7 +382,7 @@ ansible-playbook playbooks/deploy_role.yml -e 'role_name=frontend' --list-tasks
 The Ansible role structure integrates with AutoBot's deployment workflows:
 
 1. **setup.sh**: Installs Ansible and dependencies
-2. **run_autobot.sh**: Can trigger Ansible deployments
+2. **systemd services**: Manage backend/frontend lifecycle (replaces deprecated `run_autobot.sh`)
 3. **sync-to-vm.sh**: Syncs code after role deployment
 4. **Service Registry**: Feeds dynamic inventory
 

autobot-slm-backend/ansible/playbooks/deploy-development-services.yml

@@ -144,53 +144,19 @@
           - Mode: Development (hot reload enabled)
           - Environment: /opt/autobot/config/frontend-dev.env
 
-# Update run_autobot.sh to support development mode
-- name: Update AutoBot startup script for development mode
+# NOTE: run_autobot.sh is deprecated (Issue #863).
+# Development mode frontend is managed via systemd service autobot-frontend-dev.
+# No startup script modifications needed -- use systemctl directly.
+- name: Verify development services are running
   hosts: backend
   become: yes
 
   tasks:
-    - name: Backup current run_autobot.sh
-      copy:
-        src: /home/kali/Desktop/AutoBot/run_autobot.sh
-        dest: /home/kali/Desktop/AutoBot/run_autobot.sh.backup
-        remote_src: yes
-
-    - name: Update run_autobot.sh to support --dev mode for distributed architecture
-      blockinfile:
-        path: /home/kali/Desktop/AutoBot/run_autobot.sh
-        marker: "# {mark} DEVELOPMENT MODE FRONTEND MANAGEMENT"
-        block: |
-          start_frontend_dev() {
-              FRONTEND_IP=$(ansible-inventory -i ansible/inventory/production.yml --host autobot-frontend 2>/dev/null | python3 -c "import sys,json; print(json.load(sys.stdin).get('ansible_host',''))" 2>/dev/null)
-              FRONTEND_IP=${FRONTEND_IP:-{{ frontend_host }}}
-              echo "Starting Frontend Development Server on VM ${FRONTEND_IP}..."
-
-              # Start development frontend service via Ansible
-              ansible frontend -i ansible/inventory/production.yml -m systemd -a "name=autobot-frontend-dev state=restarted enabled=yes" -b
-
-              # Wait for frontend to be ready
-              echo "Waiting for frontend development server to start..."
-              sleep 10
-
-              # Test frontend availability
-              if curl -s -o /dev/null -w "%{http_code}" http://${FRONTEND_IP}:{{ frontend_port }} | grep -q "200"; then
-                  echo "Frontend development server ready at http://${FRONTEND_IP}:{{ frontend_port }}"
-              else
-                  echo "Frontend development server may not be fully ready yet"
-                  echo "   Check status with: ansible frontend -i ansible/inventory/production.yml -m shell -a 'systemctl status autobot-frontend-dev'"
-              fi
-          }
-
-          # Add frontend dev start to main dev mode function
-          if [[ "$*" == *"--dev"* ]]; then
-              start_frontend_dev
-          fi
-
-    - name: Make run_autobot.sh executable
-      file:
-        path: /home/kali/Desktop/AutoBot/run_autobot.sh
-        mode: '0755'
+    - name: Ensure autobot-backend service is running
+      systemd:
+        name: autobot-backend
+        state: started
+        enabled: yes
 
 # Display final status
 - name: Development Setup Complete
@@ -211,10 +177,10 @@
 
           Backend:
           - URL: http://{{ backend_host }}:{{ backend_port }}
-          - Service: Runs via run_autobot.sh --dev
+          - Service: autobot-backend (systemd)
 
           Usage:
-          - Start all: bash run_autobot.sh --dev
+          - Start all: sudo systemctl start autobot-backend
           - Frontend only: ansible frontend -i ansible/inventory/production.yml -m systemd -a "name=autobot-frontend-dev state=started"
           - Check status: ansible frontend -i ansible/inventory/production.yml -m shell -a "systemctl status autobot-frontend-dev"
 

docs/ROADMAP_2025.md

@@ -530,7 +530,7 @@ AUTOBOT_REASONING_MODEL=qwen3.5:9b
 
 | Task | Planned | Actual | Status |
 |------|---------|--------|--------|
-| Single-command startup | ✓ | `bash run_autobot.sh` | ✅ |
+| Single-command startup | ✓ | `systemctl start autobot-backend` | ✅ |
 | Systemd service | ✓ | Optional config | ✅ |
 | Crontab auto-start | ✓ | Optional | ✅ |
 | Graceful shutdown | ✓ | Resource cleanup | ✅ |

docs/adr/001-distributed-vm-architecture.md

@@ -83,7 +83,7 @@ We adopt a distributed 6-VM architecture where each VM serves a specific purpose
 
 ### Key Files
 
-- `run_autobot.sh` - Main startup script orchestrating all VMs
+- `scripts/start-services.sh` - CLI service wrapper (replaces deprecated `run_autobot.sh`)
 - `scripts/utilities/sync-to-vm.sh` - File synchronization utility
 - `~/.ssh/autobot_key` - SSH key for VM authentication
 

docs/adr/005-single-frontend-mandate.md

@@ -80,7 +80,7 @@ This is an absolute mandate with zero exceptions:
 
 - `sync-frontend.sh` - Quick sync script for frontend changes
 - `scripts/utilities/sync-to-vm.sh` - General purpose VM sync utility
-- `run_autobot.sh` - Orchestrates frontend startup on VM1
+- Systemd services on VM1 manage frontend startup (replaces deprecated `run_autobot.sh`)
 
 ### Forbidden Commands
 
@@ -113,7 +113,7 @@ firefox http://172.16.168.21:5173
 
 ### Enforcement
 
-The `run_autobot.sh` script enforces this by:
+The systemd service configuration enforces this by:
 1. Never starting Vite on main machine
 2. SSH to VM1 to start/restart frontend
 3. Health checking VM1's frontend server

docs/architecture/CONFIG_MIGRATION_IMPLEMENTATION.md

@@ -18,7 +18,7 @@ python scripts/validate_timeout_config.py
 # 3. Implement changes (see below)
 
 # 4. Verify no regression
-bash run_autobot.sh --dev
+scripts/start-services.sh start
 curl http://172.16.168.21:5173  # Frontend accessible?
 ```
 
@@ -409,7 +409,7 @@ curl http://localhost:8001/api/health
 curl http://172.16.168.21:5173
 
 # 5. Full system test
-bash run_autobot.sh --dev
+scripts/start-services.sh start
 # Open browser to http://172.16.168.21:5173
 # Test model selection in GUI
 ```
@@ -452,7 +452,7 @@ If issues arise:
 # Quick rollback
 git stash
 git checkout main
-bash run_autobot.sh --restart
+sudo systemctl restart autobot-backend
 
 # Or revert compatibility shim
 git checkout HEAD -- src/unified_config.py

docs/architecture/README.md

@@ -150,7 +150,7 @@ curl http://172.16.168.24:8080/api/tags
 
 | File | Purpose |
 |------|---------|
-| `run_autobot.sh` | Main startup script |
+| `scripts/start-services.sh` | CLI service wrapper (replaces deprecated `run_autobot.sh`) |
 | `.env` | Environment variables |
 | `backend/core/config.py` | Backend configuration |
 | `autobot-frontend/vite.config.ts` | Frontend configuration |

docs/architecture/SSOT_CONFIGURATION_ARCHITECTURE.md

@@ -730,7 +730,7 @@ curl -s "http://${AUTOBOT_VM_MAIN_IP}:${AUTOBOT_PORT_BACKEND}/api/health"
 
 | Script | Current Status | Required Changes |
 | ------ | -------------- | ---------------- |
-| `run_autobot.sh` | Partial SSOT | Source .env, remove hardcoded IPs |
+| ~~`run_autobot.sh`~~ | Deprecated (#863) | Replaced by systemd + `scripts/start-services.sh` |
 | `setup.sh` | Hardcoded | Source .env for all network config |
 | `scripts/utilities/sync-to-vm.sh` | Hardcoded IPs | Use AUTOBOT_VM_* variables |
 | `scripts/utilities/sync-frontend.sh` | Hardcoded | Use AUTOBOT_VM_FRONTEND_IP |

docs/architecture/VECTOR_STORE_MIGRATION.md

@@ -195,7 +195,7 @@ git checkout src/knowledge_base_v2.py
 # No action needed
 
 # 3. Restart backend
-bash run_autobot.sh --restart
+sudo systemctl restart autobot-backend
 ```
 
 ---

docs/deployment/MCP_BRIDGE_ACTIVATION.md

@@ -93,16 +93,16 @@ curl -s http://localhost:8001/api/mcp/tools | jq '.total_tools'
 ### Step 3: Graceful Backend Restart
 
 ```bash
-# Option 1: Use run_autobot.sh (recommended)
-bash run_autobot.sh --restart --dev
+# Option 1: systemd (recommended)
+sudo systemctl restart autobot-backend
 
-# Option 2: Use --verify-mcp flag for automatic verification
-bash run_autobot.sh --restart --dev --verify-mcp
+# Option 2: CLI wrapper
+scripts/start-services.sh restart
 
 # Option 3: Manual restart
 pkill -f "uvicorn backend.app:app"
 sleep 2
-bash run_autobot.sh --dev
+scripts/start-services.sh start
 ```
 
 ### Step 4: Verify New Bridge Registration
@@ -214,7 +214,7 @@ git reset --hard HEAD~1
 ### Step 3: Restart Backend
 
 ```bash
-bash run_autobot.sh --restart --dev
+sudo systemctl restart autobot-backend
 ```
 
 ### Step 4: Verify Rollback
@@ -253,7 +253,7 @@ curl -s http://localhost:8001/api/health | jq '.status'
 
 3. **Backend Not Restarted**
    ```bash
-   bash run_autobot.sh --restart
+   sudo systemctl restart autobot-backend
    ```
 
 ### Issue: 404 on Bridge Endpoint

docs/developer/AGENT_OPTIMIZATION.md

@@ -231,9 +231,9 @@ Add to GitHub Actions workflow:
     git add .claude/agents-optimized/
 ```
 
-### Startup Script Integration
+### Startup Integration
 
-Add to `run_autobot.sh`:
+Add to your service startup (e.g., systemd `ExecStartPre` or `scripts/start-services.sh`):
 
 ```bash
 # Optimize agents on startup

docs/developer/AGENT_OPTIMIZATION_SUMMARY.md

@@ -213,7 +213,7 @@ Assuming proportional token processing time:
 
 ### Startup Integration (Optional)
 
-Add to `run_autobot.sh`:
+Add to your service startup (e.g., systemd `ExecStartPre` or `scripts/start-services.sh`):
 ```bash
 # Auto-optimize agents on startup
 if [ -x "./scripts/utilities/agent-optimize.sh" ]; then

docs/developer/INFRASTRUCTURE_DEPLOYMENT.md

@@ -825,7 +825,7 @@ md5sum /home/kali/Desktop/AutoBot/autobot-backend/api/chat.py
 - [ ] All changes committed to git (local version control)
 - [ ] Services bind to `0.0.0.0` (not localhost)
 - [ ] Using `NetworkConstants` for IPs/ports (not hardcoded)
-- [ ] Tested locally first (`bash run_autobot.sh --dev`)
+- [ ] Tested locally first (`scripts/start-services.sh start` or `systemctl start autobot-backend`)
 - [ ] Synced to VMs (`./infrastructure/shared/scripts/sync-to-vm.sh`)
 - [ ] Health checks pass on all services