docs: update docs

Author: Junyi-99

README.md

@@ -1,84 +1,123 @@
-# PaperDebugger
+![branding](docs/imgs/branding.png)
 
-## Clone and Build (locally)
+PaperDebugger is an AI-powered academic writing assistant that helps researchers debug and improve their LaTeX papers. This document provides comprehensive setup and deployment instructions for the backend service.
 
-**Prequisite:**
-- `brew install bufbuild/buf/buf`
+## Overview
+The PaperDebugger backend is built with:
 
-**Clone and Build**
-```bash
-git clone https://github.com/PaperDebugger/paperdebugger.git
-cd paperdebugger
+<img src="docs/imgs/stacks.png" style="height: 200px;" />
 
-make deps  # install dependencies and libraries
-make build # build the backend
-# the binary is located in ./dist/pd.exe
+- **Language**:  Go 1.24+
+- **Framework**:  Gin (HTTP) + gRPC (API)
+- **Database**: MongoDB
+- **AI Integration**: OpenAI API
+- **Architecture**: Microservices with Protocol Buffers
+- **Authentication**: JWT-based with OAuth support
 
-cd webapp/_webapp
-npm run build:prd:chrome
-# the extension is located in wbeapp/_webapp/dist/*
-```
+## Features
 
-**Run mongodb**
+PaperDebugger never modifies your project, it only reads and provides suggestions.
 
-```bash
-docker run -d --name mongodb -p 27017:27017 mongo:latest
-```
+- **Chat**: AI-powered chats about your overleaf project
+- **Instant Insert**: One-click, insert AI response to your project
+- **Comment System**: Automatically generate comments and insert into your project
+- **Prompt Library**: Custom prompt templates for different use cases
 
-**Run backend**
+## Prerequisites
 
+### System Requirements
+- **Go**: 1.24 or higher
+- **Node.js**: LTS version (for frontend build)
+- **MongoDB**: 4.4 or higher
+- **Git**: For cloning the repository
+
+### Development Tools
+- **Buf**: Protocol Buffer compiler
+- **Wire**: Dependency injection code generator
+- **Make**: Build automation
+
+### Installation
+
+#### On macOS/Linux (using Homebrew)
 ```bash
-./dist/pd.exe
-```
+# Install Go
+brew install go
 
-## Step 1 k9s
+# Install Buf (required for Protocol Buffers)
+brew install bufbuild/buf/buf
 
-open k9s, then expose the mongo db port at 27017
-and also expose paperdebugger-mcp at 8000. (also make sure you modify the `/etc/hosts` let `127.0.0.1	paperdebugger-mcp-server`)
+# Install Node.js
+brew install node
+```
 
-## Step 2 build
+## Backend Build
 
+### 1. Clone
 ```bash
-make deps # 安装依赖
-make build
+# Clone the repository
+git clone https://github.com/PaperDebugger/paperdebugger.git
+cd paperdebugger
 ```
 
+### 2. Start MongoDB
+```bash
+# Using Docker (recommended)
+docker run -d --name mongodb -p 27017:27017 mongo:latest
+```
 
-## Step 3 run
+### 3. Setting up environments
 
 ```bash
-PD_MONGO_URI="mongodb://localhost:27017" ./dist/pd.exe
+cp .env.example .env
+# edit the .env file based on your condition
 ```
 
+### 4. Build and Run
 
-## 从克隆开始
-
-### 自动
 ```bash
-make all
+# Build the backend
+make build
+# Run the backend server
+./dist/pd.exe
 ```
 
-### 手动
+The server will start on `http://localhost:6060`.
 
-#### 0. 安装环境
+![Backend Server Running](./docs/imgs/run.png)
 
-```bash
-make deps
-```
 
-#### 1. Web 构建
+## Frontend Extension Build
 
+### Chrome Extension
 ```bash
 cd webapp/_webapp
+
+# Install frontend dependencies
 npm install
 
-npm run build:local:chrome # 构建本地版本（链接至本地后端）
-# or
-npm run build:prd:chrome # 构建生产环境版本（连接至生产环境服务器）
+# Build for production (connects to production server)
+npm run build:prd:chrome
+
+# The extension files will be in dist/
+cd dist
+zip -r paperdebugger-extension.zip *
 ```
 
-#### 2. 后端 构建
+### Installing the Extension
+1. Open Chrome and navigate to `chrome://extensions/`
+2. Enable "Developer mode"
+3. Click "Load unpacked" and select the `webapp/_webapp/dist` directory, or drag the `paperdebugger-extension.zip` file into the extensions page
 
-```bash
-make build
-```
+## Custom Endpoint Configuration
+
+If you're using PaperDebugger with Overleaf.com, ensure your backend service uses HTTPS. Chrome blocks HTTP requests from HTTPS websites for security reasons.
+
+![Custom Endpoint Configuration](./docs/imgs/custom_endpoint.png)
+
+To configure a custom endpoint:
+1. Open the PaperDebugger extension
+2. Go to Settings, click version number 5 times to enabled "Developer Tools"
+3. Enter your backend URL in the "Backend Endpoint" field
+4. Refresh the page
+
+If you encounter endpoint errors after refresh, use the "Advanced Options" at the bottom of the login page to reconfigure the endpoint.