fix(agent): register MCP tools after server initialization

Critical bug fix:
- MCP tools were never registered because servers loaded in Run()
  but tool registration happened in NewAgentLoop() with empty manager
- Move MCP tool registration from createToolRegistry to Run()
- Register MCP tools for both main agent and subag after successful server loading
- Add subagentManager field to AgentLoop for dynamic registration
- Add tool_count logging for better observability

This ensures MCP tools are properly available to both agent and subagents.

pkg/agent/loop.go

@@ -45,6 +45,7 @@ type AgentLoop struct {
 	mcpManager      *mcp.Manager           // MCP server manager for resource cleanup
 	mcpConfig       *config.Config         // Config for lazy MCP initialization
 	mcpInitOnce     sync.Once              // Ensures MCP is initialized only once
+	subagentManager *tools.SubagentManager // Subagent manager for MCP tool registration
 	running         atomic.Bool
 	summarizing     sync.Map // Tracks which sessions are currently being summarized
 	channelManager  *channels.Manager
@@ -105,22 +106,8 @@ func createToolRegistry(workspace string, restrict bool, cfg *config.Config, msg
 	})
 	registry.Register(messageTool)
 
-	// Register MCP tools from all connected servers
+	// Note: MCP tools are registered dynamically in Run() after servers are loaded
-	if mcpManager != nil {
+	// This ensures we use the agent's lifecycle context for MCP connections
-		servers := mcpManager.GetServers()
-		for serverName, conn := range servers {
-			for _, tool := range conn.Tools {
-				mcpTool := tools.NewMCPTool(mcpManager, serverName, tool)
-				registry.Register(mcpTool)
-				logger.DebugCF("agent", "Registered MCP tool",
-					map[string]interface{}{
-						"server": serverName,
-						"tool":   tool.Name,
-						"name":   mcpTool.Name(),
-					})
-			}
-		}
-	}
 
 	return registry
 }
@@ -174,6 +161,7 @@ func NewAgentLoop(cfg *config.Config, msgBus *bus.MessageBus, provider providers
 		tools:           toolsRegistry,
 		mcpManager:      mcpManager,
 		mcpConfig:       cfg, // Store config for lazy initialization in Run()
+		subagentManager: subagentManager,
 		summarizing:     sync.Map{},
 	}
 }
@@ -189,6 +177,34 @@ func (al *AgentLoop) Run(ctx context.Context) error {
 				map[string]interface{}{
 					"error": err.Error(),
 				})
+		} else {
+			// Register for both main agent and subagents
+			servers := al.mcpManager.GetServers()
+			toolCount := 0
+			for serverName, conn := range servers {
+				for _, tool := range conn.Tools {
+					mcpTool := tools.NewMCPTool(al.mcpManager, serverName, tool)
+					al.tools.Register(mcpTool)
+
+					// Also register for subagent
+					if al.subagentManager != nil {
+						al.subagentManager.RegisterTool(tools.NewMCPTool(al.mcpManager, serverName, tool))
+					}
+
+					toolCount++
+					logger.DebugCF("agent", "Registered MCP tool",
+						map[string]interface{}{
+							"server": serverName,
+							"tool":   tool.Name,
+							"name":   mcpTool.Name(),
+						})
+				}
+			}
+			logger.InfoCF("agent", "MCP tools registered successfully",
+				map[string]interface{}{
+					"server_count": len(servers),
+					"tool_count":   toolCount,
+				})
 		}
 	})