Update documentation for new features and fix outdated references

- Update deployment.md to reference new deployments/ directory structure
- Update CLI reference with new multi-user authentication system
- Add roles and permissions examples to configuration
- Fix docker-compose paths in testing documentation
- Remove references to non-existent docker-compose.test.yml
- Update troubleshooting with correct test commands
- Remove misplaced README files from test directories

docs/src/cli-reference.md

@@ -276,14 +276,26 @@ Main configuration file: `configs/config-local.yaml`
 auth:
   enabled: true
   api_keys:
-    homelab_user:
-      hash: "5e884898da28047151d0e56f8dc6292773603d0d6aabbdd62a11ef721d1542d8"
+    dev_user:
+      hash: "2baf1f40105d9501fe319a8ec463fdf4325a2a5df445adf3f572f626253678c9"
       admin: true
+      roles:
+        - admin
+      permissions:
+        '*': true
+    researcher_user:
+      hash: "ef92b778ba7a6c8f2150019a5678047b6a9a2b95cef81895吧18f9b35c54d2e3ae"
+      admin: false
+      roles:
+        - researcher
+      permissions:
+        'experiments': true
+        'datasets': true
 
 server:
   address: ":9101"
   tls:
-    enabled: true
+    enabled: false  # Set to true for production
     cert_file: "./ssl/cert.pem"
     key_file: "./ssl/key.pem"
 
@@ -294,7 +306,7 @@ security:
   ip_whitelist:
     - "127.0.0.1"
     - "::1"
-    - "192.168.0.0/16"
+    - "localhost"
     - "10.0.0.0/8"
 ```
 

docs/src/deployment.md

@@ -74,11 +74,17 @@ docker run -d \
 
 #### Docker Compose
 ```bash
-# Production mode
-docker-compose -f docker-compose.yml up -d
+# Development mode (uses root docker-compose.yml)
+docker-compose up -d
 
-# Development mode with logs
-docker-compose -f docker-compose.yml up
+# Production deployment
+docker-compose -f deployments/docker-compose.prod.yml up -d
+
+# Secure homelab deployment
+docker-compose -f deployments/docker-compose.homelab-secure.yml up -d
+
+# With custom configuration
+docker-compose -f deployments/docker-compose.prod.yml up --env-file .env.prod
 ```
 
 ### 3. Homelab Setup

docs/src/quick-start-testing.md

@@ -19,7 +19,7 @@ make self-cleanup
 
 ### 2. Start Services
 ```bash
-docker-compose -f docker-compose.prod.yml up -d
+docker-compose -f deployments/docker-compose.prod.yml up -d
 ```
 
 ### 3. Test Authentication
@@ -100,7 +100,7 @@ Tasks: X total, X queued, X running, X failed, X completed
 docker ps --filter "name=ml-"
 
 # Start services
-docker-compose -f docker-compose.prod.yml up -d
+docker-compose -f deployments/docker-compose.prod.yml up -d
 
 # Check logs
 docker logs ml-prod-api

docs/src/testing-protocol.md

@@ -74,7 +74,7 @@ echo "analysis job" | ./cli/zig-out/bin/ml queue analysis-job
 #### 3.1 Container Startup
 ```bash
 # Start production environment
-docker-compose -f docker-compose.prod.yml up -d
+docker-compose -f deployments/docker-compose.prod.yml up -d
 
 # Check container status
 docker ps --filter "name=ml-"

docs/src/troubleshooting.md

@@ -65,7 +65,7 @@ docker-compose exec redis redis-cli ping
 
 ## Development Issues
 - **Build fails**: `go mod tidy` and `cd cli && rm -rf zig-out zig-cache`
-- **Tests fail**: Start test dependencies with `docker-compose -f docker-compose.test.yml up -d`
+- **Tests fail**: Start test dependencies with `docker-compose up -d` or `make test-auth`
 
 ## CLI Issues
 - **Not found**: `cd cli && zig build dev`