Merge branch 'main' into development

Author: 4ndrelim

README.md

@@ -1,16 +1,15 @@
-![branding](docs/imgs/branding.png)
 
-**Explore the demo paper’s supporting assets in the [/demo](/demo/) folder.**
+<a href="https://chromewebstore.google.com/detail/paperdebugger/dfkedikhakpapbfcnbpmfhpklndgiaog" target="_blank"><img src="docs/imgs/branding.png" alt="PaperDebugger"/></a>
 
 <div align="center">
 <a href="https://chromewebstore.google.com/detail/paperdebugger/dfkedikhakpapbfcnbpmfhpklndgiaog" target="_blank"><img src="https://img.shields.io/chrome-web-store/users/dfkedikhakpapbfcnbpmfhpklndgiaog?label=Users" alt="Chrome Web Store Users"/></a>
 <a href="https://chromewebstore.google.com/detail/paperdebugger/dfkedikhakpapbfcnbpmfhpklndgiaog" target="_blank"><img src="https://img.shields.io/chrome-web-store/v/dfkedikhakpapbfcnbpmfhpklndgiaog?label=Chrome%20Web%20Store&logo=google-chrome&logoColor=white" alt="Chrome Web Store Version"/></a>
 <a href="https://github.com/PaperDebugger/paperdebugger/releases" target="_blank"><img src="https://img.shields.io/github/v/release/PaperDebugger/paperdebugger?label=Latest%20Release" alt="GitHub Release"/></a>
-<a href="https://github.com/PaperDebugger/paperdebugger/actions/workflows/release.yml" target="_blank"><img src="https://img.shields.io/github/actions/workflow/status/PaperDebugger/paperdebugger/build.yml?branch=main" alt="Build Status"/></a>
+<a href="https://github.com/PaperDebugger/paperdebugger/actions/workflows/build-backend-prd.yml" target="_blank"><img src="https://img.shields.io/github/actions/workflow/status/PaperDebugger/paperdebugger/build-backend-prd.yml?branch=main" alt="Build Status"/></a>
 <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 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>
+**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 our [custom MCP-based orchestration engine](demo/xtramcp/readme.md) 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">
@@ -51,7 +50,7 @@ PaperDebugger never modifies your project, it only reads and provides suggestion
 - **💬 Comment System**: Automatically generate and insert comments into your project
 - **📚 Prompt Library**: Custom prompt templates for different use cases
 - **🔒 Privacy First**: Your content stays secure - we only read, never modify
-- **🧠 Multi-Agent Orchestration** – [XtraMCP](https://github.com/PaperDebugger/xtramcp) support for literature-grounded research, AI-Conference review, citation verification, and domain-specific revision
+- **🧠 Multi-Agent Orchestration** – [XtraMCP](demo/xtramcp/readme.md) support for literature-grounded research, AI-Conference review, citation verification, and domain-specific revision
 
 https://github.com/user-attachments/assets/6c20924d-1eb6-44d5-95b0-207bd08b718b
 
@@ -64,19 +63,21 @@ https://github.com/user-attachments/assets/6c20924d-1eb6-44d5-95b0-207bd08b718b
 2. **Ready to use**
    - Open any Overleaf project
    - Click the PaperDebugger icon on the top-left
-   - Begin chatting with your LaTeX assistant!
+   - Begin chatting with your LaTeX document!
 
 ### Custom Endpoint Configuration
 
 If you want to use a **self-hosted** PaperDebugger backend, you can configure a custom endpoint. Here are the steps:
 
 1. Open the PaperDebugger extension
 
-    (a.) Go to Settings, click the version number 5 times to enable "Developer Tools" 
+    (a.) Go to Settings, click the version number **5 times** to enable "Developer Tools" 
 
     (b.) Enter your backend URL in the "Backend Endpoint" field 
 2. Refresh the page
 
+   Note: you can only use "Login by Overleaf" if you are self-hosting the backend.
+
 If you encounter endpoint errors after refresh, use the "Advanced Options" at the bottom of the login page to reconfigure.
 
 <div align="center">

demo/xtramcp/readme.md

@@ -19,13 +19,14 @@ This document describes the core tools exposed by XtraMCP and how they combine i
 | 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*! |
+| `deep_research`           | Researcher | Multi-step literature synthesis & positioning of your draft     | Local DB + retrieved papers analysis | Yes |
+| `online_search_papers`    | Researcher | Online search over external academic corpora                    | OpenReview + arXiv         | Yes |
+| `review_paper`            | Reviewer   | Conference-style structured review of a draft                   | Your draft + section-level review (static & semantic) | Yes (slightly scaled down to balance operational cost) |
+| `verify_citations`        | Reviewer   | Ensure citations are grounded, valid, and traceable             | Your draft's bibliography  | Yes |
+| `generate_citations`      | Reviewer   | Generates BibTeX-style citations by simplying providing arxiv ID / DOI / URL / title | Your draft | Yes |
 | `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)|
+| `get_user_papers`         | Misc / Researcher| Fetch all published papers with description, by a specific user | OpenReview           | Yes |
+| `search_user`             | Misc | Fetch user's profile, including info such as publications, co-authors | OpenReview                 | Yes |
 
 ---
 
@@ -122,7 +123,7 @@ Analyze and review a draft against the standards of **top-tier ML conferences**
 ## 5. `verify_citations`
 
 **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.
+Verify that citations in your draft are valid, grounded, and traceable, helping reduce the risk of desk rejection due to incorrect or unverifiable references. There have been [embarrassing cases](https://gptzero.me/news/neurips/) where accepted papers were found with hallucinated citations. This tool helps to avoid such occurrences.
 
 **How it works**:
 - Parses your bibliography and in-text citations.
@@ -137,8 +138,21 @@ Typical usage:
 - “Check whether any citations in this draft are invalid or unverifiable.”
 
 ---
+## 6. `generate_citations`
 
-## 6. `enhance_academic_writing`
+**Purpose:**
+Generate BibTeX-style citations easily by simply providing the paper's arxiv ID or DOI or URL or just its title.
+
+**How it works**:
+- Searches online for the paper's official source
+- Formats into BibTeX-style citation ready for copy-pasting
+- Inform user if proposed information is invalid / unmatched
+
+Typical usage:
+- “generate_citations: [https://arxiv.org/abs/2505.11336, ... ]”
+
+---
+## 7. `enhance_academic_writing`
 
 **Purpose:**  
 Suggest **context-aware academic writing enhancements** for selected text.
@@ -157,7 +171,7 @@ 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.”
 
-## 7. `get_user_papers`
+## 8. `get_user_papers`
 
 **Purpose:**  
 Retrieve **all papers authored by a given user** (OpenReview), identified by email.  
@@ -172,7 +186,7 @@ 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.”
 
-## 8. Conference Formatter (WIP)
+## 9. Conference Formatter (WIP)
 
 Upcoming workflows will:
 
@@ -191,7 +205,8 @@ Upcoming workflows will:
 
 - **Reviewer Flow**  
   1. Run `review_paper` on the full draft.  
-  2. For high-impact issues, call `enhance_academic_writing` on the relevant spans.  
+  2. For high-impact issues, call `enhance_academic_writing` on the relevant spans.
+  3. Verify your citations with `verify_citations` or if you haven't yet formatted them, include with `generate_citations`.
 
 - **Enhancer Flow**  
   1. Select a paragraph or section in Overleaf.  

docs/imgs/wechat.jpg

@@ -6,7 +6,7 @@ ROOT_DIR=$(cd -- "$(dirname -- "${BASH_SOURCE[0]}")/.." &>/dev/null && pwd)
 cd $ROOT_DIR
 
 OPENAI_BASE_URL=${OPENAI_BASE_URL:-https://api.openai.com/v1}
-OPENAI_API_KEY=${OPENAI_API_KEY:-sk-dummy-OPENAI_API_KEY}
+OPENAI_API_KEY=${OPENAI_API_KEY:-}
 INFERENCE_BASE_URL=${INFERENCE_BASE_URL:-https://inference.paperdebugger.workers.dev}
 INFERENCE_API_KEY=${INFERENCE_API_KEY:-sk-dummy-OPEN-ROUTER}
 MCP_BASIC_KEY=${MCP_BASIC_KEY:-sk-dummy-MCP_BASIC_KEY}

hack/prd.sh

@@ -6,7 +6,7 @@ ROOT_DIR=$(cd -- "$(dirname -- "${BASH_SOURCE[0]}")/.." &>/dev/null && pwd)
 cd $ROOT_DIR
 
 OPENAI_BASE_URL=${OPENAI_BASE_URL:-https://api.openai.com/v1}
-OPENAI_API_KEY=${OPENAI_API_KEY:-sk-dummy-OPENAI_API_KEY}
+OPENAI_API_KEY=${OPENAI_API_KEY:-}
 INFERENCE_BASE_URL=${INFERENCE_BASE_URL:-https://inference.paperdebugger.workers.dev}
 INFERENCE_API_KEY=${INFERENCE_API_KEY:-sk-dummy-OPEN-ROUTER}
 MCP_BASIC_KEY=${MCP_BASIC_KEY:-sk-dummy-MCP_BASIC_KEY}

hack/stg.sh

@@ -195,6 +195,7 @@ func (s *ChatServerV2) prepare(ctx context.Context, projectId string, conversati
 	}
 
 	var latexFullSource string
+	var projectInstructions string = ""
 	switch conversationType {
 	case chatv2.ConversationType_CONVERSATION_TYPE_DEBUG:
 		latexFullSource = "latex_full_source is not available in debug mode"
@@ -207,6 +208,8 @@ func (s *ChatServerV2) prepare(ctx context.Context, projectId string, conversati
 		if err != nil {
 			return ctx, nil, nil, err
 		}
+
+		projectInstructions = project.Instructions
 	}
 
 	var conversation *models.Conversation
@@ -217,7 +220,7 @@ func (s *ChatServerV2) prepare(ctx context.Context, projectId string, conversati
 			actor.ID,
 			projectId,
 			latexFullSource,
-			project.Instructions,
+			projectInstructions,
 			userInstructions,
 			userMessage,
 			userSelectedText,