chore: Temporary Feature Tweaks

README.md

@@ -10,7 +10,7 @@
 <a href="https://github.com/PaperDebugger/PaperDebugger?tab=AGPL-3.0-1-ov-file"><img src="https://img.shields.io/github/license/PaperDebugger/paperdebugger" alt="License"/></a>
 </div>
 
-**PaperDebugger** is an AI-powered academic writing assistant that helps researchers debug and improve their LaTeX papers with intelligent suggestions and seamless Overleaf integration. It is powered by a custom MCP-based orchestration engine that simulates the full academic workflow **Research → Critique → Revision**. <br>
+**PaperDebugger** is an AI-powered academic writing assistant that helps researchers debug and improve their research papers with intelligent suggestions and seamless Overleaf integration, without leaving the editor. It is powered by a custom MCP-based orchestration engine that simulates the full academic workflow **Research → Critique → Revision**. <br>
 This enables multi-step reasoning, reviewer-style critique, and structured revision passes beyond standard chat-based assistance.
 
 <div align="center">
@@ -25,11 +25,11 @@ This enables multi-step reasoning, reviewer-style critique, and structured revis
 
 ## 🌐 Social Media & Community Groups
 Our team is actively working to improve long-term reliability, hoping to iron out issues this month. Thank you for your patience. <br>
-Stay connected with the PaperDebugger community! Join our [Discord](https://discord.gg/WwTMzzt9xD) or WeChat channels below for updates, announcements, and support.
+Stay connected with the PaperDebugger community! Join our [Discord](https://discord.gg/WwTMzzt9xD) or WeChat channels for updates, announcements, and support.
 
 <div align="center">
-  <img src="docs/imgs/discord.png" width="40%" style="margin: 0 1.5%;"/>
-  <img src="docs/imgs/wechat.jpg" width="40%" style="margin: 0 1.5%;"/>
+  <img src="docs/imgs/discord.png" width="40%" style="margin: 0 3%;"/>
+  <img src="docs/imgs/wechat.jpg" width="40%" style="margin: 0 3%;"/>
 </div>
 
 
@@ -168,13 +168,15 @@ cp .env.example .env
 ```
 
 #### 4. Custom MCP Backend Orchestration [OPTIONAL FOR LOCAL DEV]
-Our enhanced orchestration backend, [**XtraMCP**](https://github.com/4ndrelim/academic-paper-mcp-server), is partially in-production but currently closed-source while under active development. If you wish to learn more about XtraMCP backend logic, refer to [/demo/xtramcp/readme.md](./demo/xtramcp/readme.md).<br>
+Our enhanced orchestration backend, [**XtraMCP**](https://github.com/4ndrelim/academic-paper-mcp-server), is partially deployed in-production, with selected components enabled to **balance stability and operational cost** at this stage. It is still under active development and remains closed-source for now. 
+
+To understand the backend orchestration logic and view the currently available and gated features, as well as planned capabilities, refer to [/demo/xtramcp/readme.md](./demo/xtramcp/readme.md).<br>
 You can still self-host PaperDebugger without it; all core features (chat, formatting, edits, comments) work normally.
 
 Connecting to XtraMCP unlocks:
-- research-mode agents,  
+- research-mode agents (with on-demand search for latest publications),  
 - structured reviewer-style critique,  
-- domain-specific revisions tailored to academic writing powered by [XtraGPT](https://huggingface.co/Xtra-Computing/XtraGPT-14B) models.
+- domain-specific revisions tailored for academic writing powered by [XtraGPT](https://huggingface.co/Xtra-Computing/XtraGPT-14B) models.
 
 We plan to **open-source XtraMCP** once the API stabilizes for community use.
 

demo/xtramcp/readme.md

@@ -1,36 +1,38 @@
-# XtraMCP Server – Orchestration Prompts
+# XtraMCP Orchestration Layer
 
 XtraMCP is a **custom MCP-based orchestration server** that powers PaperDebugger’s higher-level workflows:
 
-- 🧑‍🔬 **Researcher** – find and position your work within the literature  
-- 🧑‍⚖️ **Reviewer** – critique drafts like a top-tier ML reviewer  
+- 🧑‍🔬 **Researcher** – find relevant papers and position your work within the literature  
+- 🧑‍⚖️ **Reviewer** – critique drafts like a top-tier ML conference reviewer  
 - ✍️ **Enhancer** – perform fine-grained, context-aware rewrites  
 - 🧾 **Conference Formatter** (WIP) – adapt drafts to conference templates (NeurIPS, ICLR, AAAI, etc.)
 
 This document describes the core tools exposed by XtraMCP and how they combine into these workflows.
 
-> **Note:** XtraMCP is currently **closed-source** while the API and deployment story stabilize.  
+> **Note:** XtraMCP (see [4ndrelim/academic-paper-mcp-server](https://github.com/4ndrelim/academic-paper-mcp-server)) is currently **closed-source** while the API and development stabilize.  
 > PaperDebugger runs fully without it; connecting XtraMCP unlocks the advanced research/review pipelines described here.
 
 ---
 
 ## Tool Overview
 
-| Tool Name                  | Role       | Purpose                                                         | Primary Data Source         |
-|---------------------------|-----------|-----------------------------------------------------------------|-----------------------------|
-| `search_relevant_papers`  | Researcher | Fast semantic search over recent CS papers in a local vector DB, enhanced with semantic re-ranker module | Local vector database       |
-| `deep_research`           | Researcher | Multi-step literature synthesis & positioning of your draft     | Local DB + retrieved papers |
-| `online_search_papers`    | Researcher | Online search over external academic corpora                    | OpenReview + arXiv          |
-| `review_paper`            | Reviewer   | Conference-style structured review of a draft                   | Your draft                  |
-| `enhance_academic_writing`| Enhancer   | Context-aware rewriting and polishing of selected text          | Your draft + XtraGPT        |
-| `get_user_papers`| Misc | Fetch all papers, alongside description, published (OpenReview) by a specific user identified by email | User's email address
+| Tool Name                 | Role      | Purpose                                                         | Primary Data Source            | Presently Deployed    |
+|---------------------------|-----------|-----------------------------------------------------------------|--------------------------------|----------------------|
+| `search_relevant_papers`  | Researcher | Fast semantic search over recent CS papers in a local vector DB, enhanced with semantic re-ranker module | Local DB | Yes |
+| `deep_research`           | Researcher | Multi-step literature synthesis & positioning of your draft     | Local DB + retrieved papers analysis | *Temporarily Disabled* |
+| `online_search_papers`    | Researcher | Online search over external academic corpora                    | OpenReview + arXiv         | Yes (*Partially*) with arXiv |
+| `review_paper`            | Reviewer   | Conference-style structured review of a draft                   | Your draft + section-level review (static & semantic) | Yes (*Partially*) — Title, Abstract, Intro — to balance operational cost. |
+| `verify_citations`        | Reviewer   | Ensure citations are grounded, valid, and traceable             | Your draft's bibliography  | *Coming Soon*! |
+| `enhance_academic_writing`| Enhancer   | Context-aware rewriting and polishing of selected text          | Your draft + XtraGPT       | *Temporarily Disabled* |
+| `get_user_papers`         | Misc / Researcher| Fetch all published papers with description, by a specific user | OpenReview           | *Disabled* (requires auth; easy to enable with local deployment) |
+| `search_user`             | Misc | Fetch user's profile, including info such as publications, co-authors | OpenReview                 | *Disabled* (requires auth; easy to enable with local deployment)|
 
 ---
 
 ## 1. `search_relevant_papers`
 
 **Purpose:**  
-Search for similar or relevant papers by keywords or extracted concepts against a **local database of academic papers**.<br>This tool uses semantic search with vector embeddings to find the most relevant results, enhanced with a re-ranker module to better capture nuance. It is fast and the default and recommended tool for paper searches.
+Search for similar or relevant papers by keywords or extracted concepts against a **local corpus of ~800,000 academic papers**.<br>This tool uses semantic search with vector embeddings to find the most relevant results, enhanced with a re-ranker module to better capture nuance. It is fast and the default and recommended tool for paper searches.
 
 **How it works:**
 
@@ -48,7 +50,7 @@ Search for similar or relevant papers by keywords or extracted concepts against
 ## 2. `deep_research`
 
 **Purpose:**  
-Given a **research topic or draft paper**, perform multi-step literature exploration and synthesis. Summarize their findings, and provide insights on similarities and differences to assist in the research process.
+Given a **research topic or draft paper**, perform multi-step literature exploration and synthesis. Summarize their findings, and provide insights on similarities and differences to assist in the research process. This helps you to position your work.
 
 **How it works:**
 
@@ -62,7 +64,7 @@ Given a **research topic or draft paper**, perform multi-step literature explora
 **Typical usage:**
 
 - “deep_research to compare my draft to recent work on retrieval-augmented generation.”  
-- “For this topic, deep_research 5-10 relevant papers and explain where the open gaps are.”
+- “For this topic, deep_research 5-10 relevant papers and explain where the open gaps are and what I can adopt.”
 
 ---
 
@@ -117,8 +119,26 @@ Analyze and review a draft against the standards of **top-tier ML conferences**
 - “review_paper on method clarity and experimental rigor.”
 
 ---
+## 5. `verify_citations`
 
-## 5. `enhance_academic_writing`
+**Purpose:**
+Verify that citations in your draft are valid, grounded, and traceable, helping reduce the risk of desk rejection due to incorrect or unverifiable references.
+
+**How it works**:
+- Parses your bibliography and in-text citations.
+- Verifies that cited papers, preprints, and URLs:
+  - exist and are reachable,
+  - correspond to real publications or preprints,
+  - match their claimed titles/authors/venues where possible.
+- Flags any issues or un-verifiable sources.
+
+Typical usage:
+- “verify_citations”
+- “Check whether any citations in this draft are invalid or unverifiable.”
+
+---
+
+## 6. `enhance_academic_writing`
 
 **Purpose:**  
 Suggest **context-aware academic writing enhancements** for selected text.
@@ -137,7 +157,7 @@ Suggest **context-aware academic writing enhancements** for selected text.
 - "enhance_academic_writing this paragraph to be clearer and more concise, preserving all technical details.”  
 - "enhance_academic_writing the abstract to be suitable for NeurIPS.”
 
-## 6. `get_user_papers`
+## 7. `get_user_papers`
 
 **Purpose:**  
 Retrieve **all papers authored by a given user** (OpenReview), identified by email.  
@@ -152,7 +172,7 @@ Useful for quickly assembling a researcher’s publication list or grounding con
 - “get_user_papers for <author-email> in summary mode.”  
 - “Retrieve all publications by this researcher and then compare my draft using deep_research.”
 
-## 7. Conference Formatter (WIP)
+## 8. Conference Formatter (WIP)
 
 Upcoming workflows will:
 

webapp/_webapp/src/components/message-entry-container/tools/jsonrpc.tsx

@@ -12,59 +12,22 @@ type JsonRpcProps = {
 };
 
 export const JsonRpc = ({ functionName, jsonRpcResult, preparing, animated }: JsonRpcProps) => {
-  const [isCollapsed, setIsCollapsed] = useState(false);
 
   if (preparing) {
     return (
       <div className={cn("tool-card", { animated: animated })}>
         <div className="flex items-center justify-between">
-          <h3 className="tool-card-title tool-card-jsonrpc">{functionName}</h3>
+          <h3 className="tool-card-title tool-card-jsonrpc">{"Calling " + functionName}</h3>
         </div>
         <LoadingIndicator text="Processing ..." estimatedSeconds={300} />
       </div>
     );
   }
 
-  const toggleCollapse = () => {
-    setIsCollapsed(!isCollapsed);
-  };
-
   return (
     <div className={cn("tool-card noselect narrow", { animated: animated })}>
-      <div className="flex items-center justify-between cursor-pointer" onClick={toggleCollapse}>
+      <div className="flex items-center justify-between cursor-pointer">
         <h3 className="tool-card-title tool-card-jsonrpc">{functionName}</h3>
-        <button
-          className="text-gray-400 hover:text-gray-600 transition-colors duration-200 p-1 rounded"
-          aria-label={isCollapsed ? "Expand" : "Collapse"}
-        >
-          <svg
-            className={cn("w-4 h-4 transition-transform duration-200", {
-              "rotate-180": !isCollapsed,
-            })}
-            fill="none"
-            stroke="currentColor"
-            viewBox="0 0 24 24"
-          >
-            <path strokeLinecap="round" strokeLinejoin="round" strokeWidth={2} d="M19 9l-7 7-7-7" />
-          </svg>
-        </button>
-      </div>
-
-      <div
-        className={cn("canselect overflow-hidden transition-all duration-300 ease-in-out", {
-          "max-h-0 opacity-0": isCollapsed,
-          "max-h-[1000px] opacity-100": !isCollapsed,
-        })}
-      >
-        {jsonRpcResult.result && (
-          <div className="text-xs">
-            <MarkdownComponent animated={animated}>
-              {jsonRpcResult.result.content?.map((content) => content.text).join("\n") || ""}
-            </MarkdownComponent>
-          </div>
-        )}
-
-        {jsonRpcResult.error && <div className="text-xs text-red-600">{jsonRpcResult.error.message}</div>}
       </div>
     </div>
   );

webapp/_webapp/src/components/message-entry-container/tools/tools.tsx

@@ -18,16 +18,18 @@ type ToolsProps = {
 
 // define a const string list.
 const XTRA_MCP_TOOL_NAMES = [
-  // researcher tools
+  // RESEARCHER TOOLS
   "search_relevant_papers",
   "online_search_papers",
-  "deep_research",
-  // reviewer tools
+  // "deep_research",
+  // REVIEWER TOOLS
   "review_paper",
-  // enhancer tools
-  "enhance_academic_writing",
-  // misc
-  "get_user_papers",
+  // "verify_citations"
+  // ENHANCER TOOLS
+  // "enhance_academic_writing",
+  // OPENREVIEW ONLINE TOOLS
+  // "get_user_papers",
+  // "search_user"
 ];
 
 export default function Tools({ messageId, functionName, message, error, preparing, animated }: ToolsProps) {