update docs

Author: ioki-smore

docs/src/README.md

@@ -1,130 +1 @@
-# DeepTrace Documentation
-
-Welcome to the comprehensive documentation for **DeepTrace** - a cutting-edge, non-intrusive distributed tracing framework designed specifically for microservices architectures.
-
-## What is DeepTrace?
-
-**DeepTrace** is a revolutionary distributed tracing framework that enables accurate end-to-end observation of request execution paths in microservices environments **without requiring any code instrumentation**. By leveraging advanced eBPF technology and intelligent transaction semantics, DeepTrace achieves over 95% tracing accuracy even under high concurrency scenarios.
-
-### Key Innovations
-
-🚀 **Non-Intrusive Design**  
-No code changes required - DeepTrace works out of the box with your existing applications
-
-🔍 **Protocol-Aware Intelligence**  
-Supports 20+ application protocols (HTTP, gRPC, Redis, MongoDB, etc.) with intelligent parsing
-
-🧠 **Transaction-Based Correlation**  
-Uses dual-phase transaction inference with API affinity and persistent field similarity
-
-⚡ **High Performance**  
-94% reduction in transmission overhead compared to traditional tracing frameworks
-
-🎯 **Production Ready**  
-Successfully deployed across finance, e-commerce, and other industries
-
-## Architecture Overview
-
-DeepTrace consists of two main components:
-
-- **Agent**: Deployed on each host, responsible for non-intrusive request collection through eBPF
-- **Server**: Runs in Kubernetes clusters, handles trace reconstruction and provides query services
-
-```mermaid
-graph TB
-    subgraph "Host 1"
-        A1[Application 1]
-        A2[Application 2]
-        AG1[DeepTrace Agent]
-        A1 --> AG1
-        A2 --> AG1
-    end
-    
-    subgraph "Host 2"
-        A3[Application 3]
-        A4[Application 4]
-        AG2[DeepTrace Agent]
-        A3 --> AG2
-        A4 --> AG2
-    end
-    
-    subgraph "DeepTrace Server Cluster"
-        S[DeepTrace Server]
-        DB[(Elasticsearch)]
-        WEB[Web Interface]
-        S --> DB
-        S --> WEB
-    end
-    
-    AG1 --> S
-    AG2 --> S
-```
-
-## Core Features
-
-### 1. Protocol-Aware Span Construction
-- **eBPF-based packet capture** for non-intrusive monitoring
-- **Protocol templates** for accurate parsing of 20+ protocols
-- **Smart request boundary detection** using length-field jumps and full parsing
-- **Efficient span creation** with critical metadata extraction
-
-### 2. Transaction-Based Span Correlation
-- **Nested API affinity**: Traffic intensity correlations using Pearson coefficients
-- **Persistent field similarity**: TF-IDF-weighted cosine similarity for transaction field isolation
-- **Entropy-weighted adaptive scoring**: Intelligent fusion of transaction semantics and causality metrics
-- **15% reduction in misattributions** compared to traditional delay/FIFO methods
-
-### 3. Query-Driven Trace Assembly
-- **On-host compression** and **dual-indexing** for minimal overhead
-- **Iterative trace reconstruction** based on operator queries
-- **Tag-based inverted indexes** and **metric histograms**
-- **94% reduction in transmission overhead** while maintaining query flexibility
-
-## Quick Navigation
-
-### 🚀 Getting Started
-New to DeepTrace? Start here:
-- [Quick Start Guide](./getting-started/quick-start.md) - Get up and running in 10 minutes
-- [Installation](./getting-started/installation.md) - Detailed installation instructions
-- [All-in-One Deployment](./getting-started/all-in-one.md) - Single-host setup for testing
-
-### 📖 User Guide
-Learn how to use DeepTrace effectively:
-- [Basic Usage](./user-guide/basic-usage.md) - Essential operations and workflows
-- [Deployment Modes](./user-guide/deployment-modes.md) - Choose the right deployment strategy
-- [Trace Analysis](./user-guide/trace-analysis.md) - Analyze and interpret traces
-
-### 🏗️ Architecture & Implementation
-Understand how DeepTrace works:
-- [System Overview](./architecture/overview.md) - High-level architecture
-- [eBPF Implementation](./ebpf/overview.md) - Deep dive into eBPF components
-- [Advanced Topics](./advanced/correlation-algorithms.md) - Advanced features and algorithms
-
-### 🔧 Development & Testing
-For developers and contributors:
-- [Testing Guide](./testing/overview.md) - Comprehensive testing strategies
-- [API Reference](./api/agent.md) - Complete API documentation
-- [Troubleshooting](./troubleshooting/common-issues.md) - Common issues and solutions
-
-## Supported Environments
-
-DeepTrace has been tested and verified on:
-
-- **Operating System**: Ubuntu 24.04 LTS
-- **Kernel Version**: 6.8.0-55-generic or later
-- **Container Runtime**: Docker v26.1.3+
-- **Orchestration**: Kubernetes 1.20+
-
-## Community & Support
-
-- **GitHub Repository**: [DeepShield-AI/DeepTrace](https://github.com/DeepShield-AI/DeepTrace)
-- **Issues & Bug Reports**: [GitHub Issues](https://github.com/DeepShield-AI/DeepTrace/issues)
-- **Discussions**: [GitHub Discussions](https://github.com/DeepShield-AI/DeepTrace/discussions)
-
-## License
-
-DeepTrace is released under the [MIT License](./appendix/license.md).
-
----
-
-Ready to get started? Jump to our [Quick Start Guide](./getting-started/quick-start.md) and have DeepTrace running in minutes!
+# Introduction

docs/src/SUMMARY.md

@@ -1,6 +1,6 @@
 # Summary
 
-[Introduction](./README.md)
+[Introduction](./introduction.md)
 
 ---
 

docs/src/getting-started/configuration.md

@@ -24,10 +24,8 @@ server/config/config.toml
 
 DeepTrace provides several example configurations:
 
-- `config.toml.example` - Basic configuration template
+- `deeptrace.toml.example` - Basic configuration template
 - `full.toml` - Complete configuration with all options
-- `production.toml` - Production-ready configuration
-- `development.toml` - Development environment settings
 
 ## Required Configuration
 
@@ -96,77 +94,6 @@ workers = 16
 ip = "0.0.0.0"
 port = 7901
 path = "deeptrace/ws"
-
-# Additional server settings
-max_connections = 1000
-connection_timeout = 30
-heartbeat_interval = 10
-```
-
-### DeepTrace Service
-
-```toml
-# DeepTrace agent service port
-deeptrace_port = 52001
-
-# Service configuration
-[service]
-log_level = "info"
-log_file = "/var/log/deeptrace/agent.log"
-pid_file = "/var/run/deeptrace/agent.pid"
-```
-
-### Agent Performance Settings
-
-```toml
-[agents]
-# Span processing configuration
-[agents.span]
-batch_size = 1024
-flush_interval = 5
-max_queue_size = 10000
-
-# Data sender configuration
-[agents.sender]
-mem_buffer_size = 16      # MB
-file_buffer_size = 32     # MB
-file_size_limit = 1024    # MB
-batch_size = 1024
-compression = true
-retry_attempts = 3
-retry_delay = 1000        # milliseconds
-
-# Trace collection settings
-[agents.trace]
-# Specific PIDs to monitor (empty = monitor all Docker containers)
-pids = []
-
-# Process filtering
-include_processes = ["nginx", "redis", "mongodb"]
-exclude_processes = ["systemd", "kernel"]
-
-# Protocol detection
-auto_detect_protocols = true
-supported_protocols = ["http", "grpc", "redis", "mongodb", "mysql"]
-```
-
-### API Configuration
-
-```toml
-[agents.api]
-# API server settings
-port = 7899
-address = "0.0.0.0"
-workers = 1
-ident = "deeptrace"
-
-# API security
-enable_auth = false
-api_key = "your_api_key_here"
-
-# Rate limiting
-rate_limit = 1000  # requests per minute
-burst_limit = 100
 ```
 
 ## Advanced Configuration
@@ -274,23 +201,6 @@ ssh_port = 22
 ssh_key_path = "/home/deeptrace/.ssh/id_rsa"
 ```
 
-#### TLS Configuration
-
-Enable TLS for secure communication:
-
-```toml
-[server.tls]
-enabled = true
-cert_file = "/etc/deeptrace/certs/server.crt"
-key_file = "/etc/deeptrace/certs/server.key"
-ca_file = "/etc/deeptrace/certs/ca.crt"
-
-[elastic.tls]
-enabled = true
-verify_certificates = true
-ca_file = "/etc/elasticsearch/certs/ca.crt"
-```
-
 ## Environment Variables
 
 DeepTrace supports environment variable substitution in configuration files:
@@ -347,8 +257,6 @@ Error: Cannot connect to Elasticsearch at localhost:9200
 ### 1. Security
 
 - **Use environment variables** for sensitive information
-- **Enable TLS** for production deployments
-- **Use SSH keys** instead of passwords
 - **Restrict network access** to DeepTrace ports
 
 ### 2. Performance
@@ -372,75 +280,6 @@ Error: Cannot connect to Elasticsearch at localhost:9200
 - **Test configuration changes** in development first
 - **Keep backups** of working configurations
 
-## Configuration Templates
-
-### Small Deployment (1-5 hosts)
-
-```toml
-[server]
-ip = "192.168.1.100"
-port = 7901
-
-[elastic]
-elastic_password = "simple_password"
-bulk_size = 512
-
-[[agents.agent_info]]
-agent_name = "small-deployment"
-user_name = "ubuntu"
-host_ip = "192.168.1.101"
-ssh_port = 22
-host_password = "password"
-workers = 4
-
-[agents.sender]
-batch_size = 512
-mem_buffer_size = 16
-```
-
-### Medium Deployment (5-20 hosts)
-
-```toml
-[server]
-ip = "deeptrace.internal.com"
-port = 7901
-
-[elastic]
-elastic_password = "${ELASTIC_PASSWORD}"
-bulk_size = 1024
-request_timeout = 20
-
-# Multiple agents configuration...
-[agents.sender]
-batch_size = 1024
-mem_buffer_size = 32
-compression = true
-```
-
-### Large Deployment (20+ hosts)
-
-```toml
-[server]
-ip = "deeptrace-cluster.company.com"
-port = 7901
-max_connections = 5000
-
-[elastic]
-elastic_password = "${ELASTIC_PASSWORD}"
-bulk_size = 2048
-request_timeout = 30
-
-[agents.sender]
-batch_size = 2048
-mem_buffer_size = 64
-file_buffer_size = 128
-compression = true
-
-[logging]
-level = "warn"
-file = "/var/log/deeptrace/production.log"
-```
-
 ## Troubleshooting Configuration
 
 ### Common Issues
@@ -476,8 +315,4 @@ After configuring DeepTrace:
 
 1. **[All-in-One Deployment](./all-in-one.md)**: Deploy for testing
 2. **[Basic Usage](../user-guide/basic-usage.md)**: Start using DeepTrace
-3. **[Troubleshooting](../troubleshooting/common-issues.md)**: Resolve issues
-
----
-
-Proper configuration is crucial for DeepTrace's performance and reliability. Take time to understand each setting and adjust them according to your specific requirements and environment.
+3. **[Troubleshooting](../troubleshooting/common-issues.md)**: Resolve issues