fix: ConfigService now reads subsystems from database

Critical regression fix - subsystems were hardcoded instead of reading user settings.
Added CreateDefaultSubsystems to queries/subsystems.go.
ConfigService now queries agent_subsystems table for actual user configuration.
AgentLifecycleService creates default subsystems when creating new agents.
Respects user-configured enabled/auto_run settings from UI.

aggregator-server/internal/database/queries/subsystems.go

@@ -280,6 +280,23 @@ func (q *SubsystemQueries) DeleteSubsystem(agentID uuid.UUID, subsystem string)
 	return nil
 }
 
+// CreateDefaultSubsystems creates default subsystems for a new agent
+func (q *SubsystemQueries) CreateDefaultSubsystems(agentID uuid.UUID) error {
+	defaults := []models.AgentSubsystem{
+		{AgentID: agentID, Subsystem: "updates", Enabled: true, AutoRun: true, IntervalMinutes: 60},
+		{AgentID: agentID, Subsystem: "storage", Enabled: true, AutoRun: true, IntervalMinutes: 5},
+		{AgentID: agentID, Subsystem: "system", Enabled: true, AutoRun: true, IntervalMinutes: 5},
+		{AgentID: agentID, Subsystem: "docker", Enabled: true, AutoRun: true, IntervalMinutes: 15},
+	}
+
+	for _, sub := range defaults {
+		if err := q.CreateSubsystem(&sub); err != nil {
+			return fmt.Errorf("failed to create subsystem %s: %w", sub.Subsystem, err)
+		}
+	}
+	return nil
+}
+
 // Helper function to join update statements
 func joinUpdates(updates []string) string {
 	result := ""

aggregator-server/internal/services/agent_lifecycle.go

@@ -7,6 +7,7 @@ import (
 	"time"
 
 	"github.com/Fimeg/RedFlag/aggregator-server/internal/config"
+	"github.com/Fimeg/RedFlag/aggregator-server/internal/database/queries"
 	"github.com/Fimeg/RedFlag/aggregator-server/internal/models"
 	"github.com/google/uuid"
 	"github.com/jmoiron/sqlx"
@@ -35,12 +36,13 @@ type AgentConfig struct {
 
 // AgentLifecycleService manages all agent lifecycle operations
 type AgentLifecycleService struct {
-	db              *sqlx.DB
-	config          *config.Config
-	buildService    *BuildService
-	configService   *ConfigService
-	artifactService *ArtifactService
-	logger          *log.Logger
+	db               *sqlx.DB
+	config           *config.Config
+	buildService     *BuildService
+	configService    *ConfigService
+	artifactService  *ArtifactService
+	subsystemQueries *queries.SubsystemQueries
+	logger           *log.Logger
 }
 
 // NewAgentLifecycleService creates a new lifecycle service
@@ -50,12 +52,13 @@ func NewAgentLifecycleService(
 	logger *log.Logger,
 ) *AgentLifecycleService {
 	return &AgentLifecycleService{
-		db:              db,
-		config:          cfg,
-		buildService:    NewBuildService(db, cfg, logger),
-		configService:   NewConfigService(db, cfg, logger),
-		artifactService: NewArtifactService(db, cfg, logger),
-		logger:          logger,
+		db:               db,
+		config:           cfg,
+		buildService:     NewBuildService(db, cfg, logger),
+		configService:    NewConfigService(db, cfg, logger),
+		artifactService:  NewArtifactService(db, cfg, logger),
+		subsystemQueries: queries.NewSubsystemQueries(db),
+		logger:           logger,
 	}
 }
 
@@ -190,7 +193,17 @@ func (s *AgentLifecycleService) createAgent(
 		VALUES (:id, :hostname, :os_type, :agent_version, :machine_id, :created_at, :updated_at)
 	`
 	_, err := s.db.NamedExecContext(ctx, query, agent)
-	return err
+	if err != nil {
+		return fmt.Errorf("agent record creation failed: %w", err)
+	}
+
+	// Create default subsystems for new agent
+	if err := s.subsystemQueries.CreateDefaultSubsystems(agent.ID); err != nil {
+		s.logger.Printf("Warning: failed to create default subsystems: %v", err)
+		// Non-fatal error - agent still created
+	}
+
+	return nil
 }
 
 // updateAgent updates existing agent record

aggregator-server/internal/services/config_service.go

@@ -8,6 +8,7 @@ import (
 	"time"
 
 	"github.com/Fimeg/RedFlag/aggregator-server/internal/config"
+	"github.com/Fimeg/RedFlag/aggregator-server/internal/database/queries"
 	"github.com/Fimeg/RedFlag/aggregator-server/internal/models"
 	"github.com/google/uuid"
 	"github.com/jmoiron/sqlx"
@@ -15,17 +16,19 @@ import (
 
 // ConfigService manages agent configuration generation and validation
 type ConfigService struct {
-	db     *sqlx.DB
-	config *config.Config
-	logger *log.Logger
+	db               *sqlx.DB
+	config           *config.Config
+	logger           *log.Logger
+	subsystemQueries *queries.SubsystemQueries
 }
 
 // NewConfigService creates a new configuration service
 func NewConfigService(db *sqlx.DB, cfg *config.Config, logger *log.Logger) *ConfigService {
 	return &ConfigService{
-		db:     db,
-		config: cfg,
-		logger: logger,
+		db:               db,
+		config:           cfg,
+		logger:           logger,
+		subsystemQueries: queries.NewSubsystemQueries(db),
 	}
 }
 
@@ -58,6 +61,27 @@ func (s *ConfigService) GenerateNewConfig(agentCfg *AgentConfig) ([]byte, error)
 		serverURL = s.config.Server.PublicURL
 	}
 
+	// Get subsystems from database (not hardcoded!)
+	agentID := uuid.MustParse(agentCfg.AgentID)
+	subsystems, err := s.subsystemQueries.GetSubsystems(agentID)
+	if err != nil || len(subsystems) == 0 {
+		// If not found, create defaults
+		if err := s.subsystemQueries.CreateDefaultSubsystems(agentID); err != nil {
+			return nil, fmt.Errorf("failed to create default subsystems: %w", err)
+		}
+		subsystems, _ = s.subsystemQueries.GetSubsystems(agentID)
+	}
+
+	// Convert to map format for JSON
+	subsystemMap := make(map[string]interface{})
+	for _, sub := range subsystems {
+		subsystemMap[sub.Subsystem] = map[string]interface{}{
+			"enabled":  sub.Enabled,
+			"auto_run": sub.AutoRun,
+			"interval": sub.IntervalMinutes,
+		}
+	}
+
 	cfg := &AgentConfigData{
 		AgentID:   agentCfg.AgentID,
 		Version:   agentCfg.Version,
@@ -69,12 +93,7 @@ func (s *ConfigService) GenerateNewConfig(agentCfg *AgentConfig) ([]byte, error)
 			"updates":  3600, // 1 hour
 			"commands": 30,   // 30 seconds
 		},
-		Subsystems: map[string]interface{}{
-			"updates": map[string]interface{}{"enabled": true, "auto_run": true, "timeout": 300},
-			"storage": map[string]interface{}{"enabled": true, "auto_run": true, "timeout": 60},
-			"system":  map[string]interface{}{"enabled": true, "auto_run": true, "timeout": 60},
-			"docker":  map[string]interface{}{"enabled": true, "auto_run": true, "timeout": 120},
-		},
+		Subsystems:     subsystemMap, // ← USE DATABASE VALUES!
 		MaxRetries:     3,
 		TimeoutSeconds: 30,
 		MachineID:      agentCfg.MachineID,