feat: Update library tool prompts

internal/api/user/list_prompts.go

@@ -18,33 +18,49 @@ var defaultPrompts = []*userv1.Prompt{
 	// 	CreatedAt:    timestamppb.New(time.Time{}),
 	// 	UpdatedAt:    timestamppb.New(time.Time{}),
 	// 	Title:        "Enhance Academic Writing (Powered by XtraGPT)",
-	// 	Content:      "Suggest context-aware academic paper writing enhancements for selected text.",
+	// 	Content:      "Suggest context-aware academic paper writing enhancements for the selected text.",
 	// 	IsUserPrompt: false,
 	// },
 	{
 		Id:           "2",
 		CreatedAt:    timestamppb.New(time.Time{}),
 		UpdatedAt:    timestamppb.New(time.Time{}),
-		Title:        "Review (Powered by XtraMCP)",
-		Content:      "Review my paper and identify issues",
+		Title:        "Search Relevant Papers (Powered by XtraMCP)",
+		Content:      "First, understand my paper and extract the key ideas into an optimized query to find papers that are relevant to my work. Then search for relevant papers to read.\n\nOptional Args:\ntop_k: 10\nStart Date: None (e.g. 2018-12-31)\nEnd Date: None (e.g. 2025-12-31)",
 		IsUserPrompt: false,
 	},
 	{
 		Id:           "3",
 		CreatedAt:    timestamppb.New(time.Time{}),
 		UpdatedAt:    timestamppb.New(time.Time{}),
-		Title:        "Find Relevant Papers (Powered by XtraMCP)",
-		Content:      "Find me relevant papers to read",
+		Title:        "Paper Review (Powered by XtraMCP)",
+		Content:      "Call review_paper and evaluate my paper.\n\nOptional Args:\nTarget Venue: None (e.g. ICML, NeurIPS, CVPR)\nSeverity Level (blocker | major | minor | nit): Major\nSpecific Sections (default: entire paper): None (e.g. Abstract, Results, <section name in paper>)",
+		IsUserPrompt: false,
+	},
+	{
+		Id:           "4",
+		CreatedAt:    timestamppb.New(time.Time{}),
+		UpdatedAt:    timestamppb.New(time.Time{}),
+		Title:        "Verify Citations (Powered by XtraMCP)",
+		Content:      "Call verify_citations to check the validity of all citations in my paper and identify any potential issues such as incorrect formatting, missing information, or inaccurate references.",
+		IsUserPrompt: false,
+	},
+	{
+		Id:           "5",
+		CreatedAt:    timestamppb.New(time.Time{}),
+		UpdatedAt:    timestamppb.New(time.Time{}),
+		Title:        "Deep Research (Powered by XtraMCP)",
+		Content:      "First, understand my paper and extract the key ideas into an optimized query. Do deep research and compare my papers against others.",
+		IsUserPrompt: false,
+	},
+	{
+		Id:           "6",
+		CreatedAt:    timestamppb.New(time.Time{}),
+		UpdatedAt:    timestamppb.New(time.Time{}),
+		Title:        "Online Research (Powered by XtraMCP)",
+		Content:      "Understand my paper and run online search to find the latest papers related to my work.",
 		IsUserPrompt: false,
 	},
-	// {
-	// 	Id:           "4",
-	// 	CreatedAt:    timestamppb.New(time.Time{}),
-	// 	UpdatedAt:    timestamppb.New(time.Time{}),
-	// 	Title:        "Deep Research (Powered by XtraMCP)",
-	// 	Content:      "Do deep research and compare my papers against others",
-	// 	IsUserPrompt: false,
-	// },
 }
 
 func (s *UserServer) ListPrompts(

internal/services/toolkit/client/utils.go

@@ -12,7 +12,6 @@ import (
 	"paperdebugger/internal/libs/logger"
 	"paperdebugger/internal/services"
 	"paperdebugger/internal/services/toolkit/registry"
-	"paperdebugger/internal/services/toolkit/tools/xtramcp"
 	chatv1 "paperdebugger/pkg/gen/api/chat/v1"
 
 	"github.com/openai/openai-go/v2"
@@ -105,25 +104,25 @@ func initializeToolkit(
 ) *registry.ToolRegistry {
 	toolRegistry := registry.NewToolRegistry()
 
-	// Load tools dynamically from backend
-	xtraMCPLoader := xtramcp.NewXtraMCPLoader(db, projectService, cfg.XtraMCPURI)
+	// // Load tools dynamically from backend
+	// xtraMCPLoader := xtramcp.NewXtraMCPLoader(db, projectService, cfg.XtraMCPURI)
 
-	// initialize MCP session first and log session ID
-	sessionID, err := xtraMCPLoader.InitializeMCP()
-	if err != nil {
-		logger.Errorf("[XtraMCP Client] Failed to initialize XtraMCP session: %v", err)
-		// TODO: Fallback to static tools or exit?
-	} else {
-		logger.Info("[XtraMCP Client] XtraMCP session initialized", "sessionID", sessionID)
+	// // initialize MCP session first and log session ID
+	// sessionID, err := xtraMCPLoader.InitializeMCP()
+	// if err != nil {
+	// 	logger.Errorf("[XtraMCP Client] Failed to initialize XtraMCP session: %v", err)
+	// 	// TODO: Fallback to static tools or exit?
+	// } else {
+	// 	logger.Info("[XtraMCP Client] XtraMCP session initialized", "sessionID", sessionID)
 
-		// dynamically load all tools from XtraMCP backend
-		err = xtraMCPLoader.LoadToolsFromBackend(toolRegistry)
-		if err != nil {
-			logger.Errorf("[XtraMCP Client] Failed to load XtraMCP tools: %v", err)
-		} else {
-			logger.Info("[XtraMCP Client] Successfully loaded XtraMCP tools")
-		}
-	}
+	// 	// dynamically load all tools from XtraMCP backend
+	// 	err = xtraMCPLoader.LoadToolsFromBackend(toolRegistry)
+	// 	if err != nil {
+	// 		logger.Errorf("[XtraMCP Client] Failed to load XtraMCP tools: %v", err)
+	// 	} else {
+	// 		logger.Info("[XtraMCP Client] Successfully loaded XtraMCP tools")
+	// 	}
+	// }
 
 	return toolRegistry
 }

internal/services/toolkit/client/utils_v2.go

@@ -13,6 +13,7 @@ import (
 	"paperdebugger/internal/libs/logger"
 	"paperdebugger/internal/services"
 	"paperdebugger/internal/services/toolkit/registry"
+	"paperdebugger/internal/services/toolkit/tools/xtramcp"
 	chatv2 "paperdebugger/pkg/gen/api/chat/v2"
 	"strings"
 	"time"
@@ -144,22 +145,22 @@ func initializeToolkitV2(
 
 	logger.Info("[AI Client V2] Registered static LaTeX tools", "count", 0)
 
-	// // Load tools dynamically from backend
-	// xtraMCPLoader := xtramcp.NewXtraMCPLoaderV2(db, projectService, cfg.XtraMCPURI)
-
-	// // initialize MCP session first and log session ID
-	// sessionID, err := xtraMCPLoader.InitializeMCP()
-	// if err != nil {
-	// 	logger.Errorf("[XtraMCP Client] Failed to initialize XtraMCP session: %v", err)
-	// } else {
-	// 	logger.Info("[XtraMCP Client] XtraMCP session initialized", "sessionID", sessionID)
-
-	// 	// dynamically load all tools from XtraMCP backend
-	// 	err = xtraMCPLoader.LoadToolsFromBackend(toolRegistry)
-	// 	if err != nil {
-	// 		logger.Errorf("[XtraMCP Client] Failed to load XtraMCP tools: %v", err)
-	// 	}
-	// }
+	// Load tools dynamically from backend
+	xtraMCPLoader := xtramcp.NewXtraMCPLoaderV2(db, projectService, cfg.XtraMCPURI)
+
+	// initialize MCP session first and log session ID
+	sessionID, err := xtraMCPLoader.InitializeMCP()
+	if err != nil {
+		logger.Errorf("[XtraMCP Client] Failed to initialize XtraMCP session: %v", err)
+	} else {
+		logger.Info("[XtraMCP Client] XtraMCP session initialized", "sessionID", sessionID)
+
+		// dynamically load all tools from XtraMCP backend
+		err = xtraMCPLoader.LoadToolsFromBackend(toolRegistry)
+		if err != nil {
+			logger.Errorf("[XtraMCP Client] Failed to load XtraMCP tools: %v", err)
+		}
+	}
 
 	return toolRegistry
 }

internal/services/toolkit/handler/toolcall_v2.go

@@ -2,9 +2,11 @@ package handler
 
 import (
 	"context"
+	"encoding/json"
 	"fmt"
 	"paperdebugger/internal/services/toolkit/registry"
 	chatv2 "paperdebugger/pkg/gen/api/chat/v2"
+	"strings"
 	"time"
 
 	"github.com/openai/openai-go/v3"
@@ -73,12 +75,128 @@ func (h *ToolCallHandlerV2) HandleToolCallsV2(ctx context.Context, toolCalls []o
 
 		toolResult, err := h.Registry.Call(ctx, toolCall.ID, toolCall.Name, []byte(toolCall.Arguments))
 
+		// Try to parse as XtraMCP ToolResult format
+		// This allows XtraMCP tools to use the new format while other tools continue with existing behavior
+		// NOTE: there is a bit of a coupled ugly logic here. (TODO: consider new API design later)
+		// 1. We rely on the xtramcp/tool_v2.go call method to return "" for LLM instruction
+		// 2. so in registry/registry_v2.go, the returned toolResult is the raw string from the tool execution
+		// 3. presently, it is not possible to do the parsing earlier in xtramcp/tool_v2.go because of the following branching logic
+		parsedXtraMCPResult, isXtraMCPFormat, parseErr := ParseXtraMCPToolResult(toolResult)
+
+		var llmContent string         // Content to send to LLM (OpenAI chat history)
+		var frontendToolResult string // Content to send to frontend (via stream)
+
+		if parseErr != nil || !isXtraMCPFormat {
+			// for non-XtraMCP tool - use existing behavior unchanged
+			llmContent = toolResult
+			frontendToolResult = toolResult
+		} else {
+			// XtraMCP ToolResult format detected - apply specialized logic
+
+			// BRANCH 1: Handle errors (success=false)
+			if !parsedXtraMCPResult.Success {
+				// Send error message to LLM
+				if parsedXtraMCPResult.Error != nil {
+					llmContent = *parsedXtraMCPResult.Error
+				} else {
+					llmContent = "Tool execution failed (no error message provided)"
+				}
+
+				// Send error payload to frontend
+				frontendPayload := map[string]interface{}{
+					"schema_version": parsedXtraMCPResult.SchemaVersion,
+					"display_mode":   parsedXtraMCPResult.DisplayMode,
+					"success":        false,
+					"metadata":       parsedXtraMCPResult.Metadata,
+				}
+				if parsedXtraMCPResult.Error != nil {
+					frontendPayload["error"] = *parsedXtraMCPResult.Error
+				}
+				frontendBytes, _ := json.Marshal(frontendPayload)
+				frontendToolResult = string(frontendBytes)
+
+			} else if parsedXtraMCPResult.DisplayMode == "verbatim" {
+				// BRANCH 2: Verbatim mode (success=true)
+
+				// check if content is truncated, use full_content if available for updating LLM context
+				contentForLLM := parsedXtraMCPResult.GetFullContentAsString()
+
+				//TODO better handle this: truncate if too long for LLM context
+				// this is a SAFEGUARD against extremely long tool outputs
+				// est 30k tokens, 4 chars/token = 120k chars
+				const maxLLMContentLen = 120000
+				contentForLLM = TruncateContent(contentForLLM, maxLLMContentLen)
+
+				// If instructions provided, send as structured payload
+				// Otherwise send raw content
+				if parsedXtraMCPResult.Instructions != nil && strings.TrimSpace(*parsedXtraMCPResult.Instructions) != "" {
+					llmContent = FormatPrompt(
+						toolCall.Name,
+						*parsedXtraMCPResult.Instructions,
+						parsedXtraMCPResult.GetMetadataValuesAsString(),
+						contentForLLM,
+					)
+				} else {
+					llmContent = contentForLLM
+				}
+
+				frontendMetadata := make(map[string]interface{})
+				if parsedXtraMCPResult.Metadata != nil {
+					for k, v := range parsedXtraMCPResult.Metadata {
+						frontendMetadata[k] = v
+					}
+				}
+
+				frontendPayload := map[string]interface{}{
+					"schema_version": parsedXtraMCPResult.SchemaVersion,
+					"display_mode":   "verbatim",
+					"content":        parsedXtraMCPResult.GetContentAsString(),
+					"success":        true,
+				}
+				if len(frontendMetadata) > 0 {
+					frontendPayload["metadata"] = frontendMetadata
+				}
+				frontendBytes, _ := json.Marshal(frontendPayload)
+				frontendToolResult = string(frontendBytes)
+
+			} else if parsedXtraMCPResult.DisplayMode == "interpret" {
+				// BRANCH 3: Interpret mode (success=true)
+
+				// LLM gets content + optional instructions for reformatting
+				if parsedXtraMCPResult.Instructions != nil && strings.TrimSpace(*parsedXtraMCPResult.Instructions) != "" {
+					llmContent = FormatPrompt(
+						toolCall.Name,
+						*parsedXtraMCPResult.Instructions,
+						parsedXtraMCPResult.GetMetadataValuesAsString(),
+						parsedXtraMCPResult.GetFullContentAsString(),
+					)
+				} else {
+					llmContent = parsedXtraMCPResult.GetFullContentAsString()
+				}
+
+				// Frontend gets minimal display (LLM will provide formatted response)
+				frontendPayload := map[string]interface{}{
+					"schema_version": parsedXtraMCPResult.SchemaVersion,
+					"display_mode":   "interpret",
+					"success":        true,
+				}
+				if parsedXtraMCPResult.Metadata != nil {
+					frontendPayload["metadata"] = parsedXtraMCPResult.Metadata
+				}
+				frontendBytes, _ := json.Marshal(frontendPayload)
+				frontendToolResult = string(frontendBytes)
+			}
+		}
+
+		// Send result to stream handler (frontend)
 		if streamHandler != nil {
-			streamHandler.SendToolCallEnd(toolCall, toolResult, err)
+			streamHandler.SendToolCallEnd(toolCall, frontendToolResult, err)
 		}
 
-		resultStr := toolResult
+		// Prepare content for LLM (OpenAI chat history)
+		resultStr := llmContent
 		if err != nil {
+			// Tool execution error (different from ToolResult.success=false)
 			resultStr = "Error: " + err.Error()
 		}
 
@@ -108,7 +226,7 @@ func (h *ToolCallHandlerV2) HandleToolCallsV2(ctx context.Context, toolCalls []o
 		if err != nil {
 			toolCallMsg.Error = err.Error()
 		} else {
-			toolCallMsg.Result = resultStr
+			toolCallMsg.Result = frontendToolResult
 		}
 
 		inappChatHistory = append(inappChatHistory, chatv2.Message{