remove sd (#15)

Author: Linbo-Liu

.gitignore

@@ -13,8 +13,5 @@ __pycache__/
 /build
 log.*
 
-# Java Files
-src/self_debug/lang/java/native/target
-
 /.idea
 src/logs

README.md

@@ -37,38 +37,135 @@
 
 🚀 Repository for automated Java code migration research, part of the [MigrationBench](https://huggingface.co/collections/AmazonScience/migrationbench-68125452fc21a4564b92b6c3) project.
 
+<!-- toc -->
 
-## 📦 Packages
+- [1. Overview](#1-overview)
+- [2. MigrationBench Datasets](#2-migrationbench-datasets)
+- [3. Installation](#3-installation)
+  * [3.1 Prerequisites](#31-prerequisites)
+  * [3.2 Install Package](#32-install-package)
+- [4. Usage](#4-usage)
+  * [4.1 Agent Types](#41-agent-types)
+  * [4.2 Running Migration](#42-running-migration)
+  * [4.3 Command Line Options](#43-command-line-options)
+- [5. Data](#5-data)
+- [6. Resources](#6-resources)
+- [7. Citation](#7-citation)
 
-This repository contains **two** sub-packages to conduct Java code migration with LLMs:
+<!-- tocstop -->
 
-### 1. 🤖 [JavaMigrationAgent](./java_migration_agent)
+## 1. Overview
 
-[**JavaMigrationAgent**](./java_migration_agent) is an LLM-based agent to automate Java 8 to Java 17 (21) migration,
-built on top of the [Strands Agents](https://strandsagents.com/latest/) framework.
+**JavaMigrationAgent** is a library for automated code migration from Java 8 to Java 17 (21) using LLM-based agents built on the [Strands Agents](https://strandsagents.com/latest/) framework.
 
-- It supports multiple migration strategies including baseline, PE (prompt engineering), RAG, and a hybrid approach (More cost effective).
+It provides multiple agent strategies for migration:
+1. **Baseline**: Direct LLM-based migration
+1. **PE (Prompt Engineering)** (Baseline + PE): Baseline with enhanced prompts for dependency updates
+1. **RAG** (Baseline + PE + RAG): Uses retrieval-augmented generation for dependency version lookup
+1. **Hybrid** (Seed change, followed by baseline + PE): Pre-processes dependencies before LLM migration (More cost effective)
 
-### 2. 🔧 [SDFeedback](./self_debug)
+The agent relies on the [MigrationBench](https://github.com/amazon-science/MigrationBench) package for evaluation.
 
-[**SDFeedback**](./self_debug) runs code migration implementation with LLMs by providing self debugging feedback,
-motivated by the [Teaching Large Language Models to Self-Debug](https://arxiv.org/abs/2304.05128) paper.
+## 2. [🤗 MigrationBench](https://huggingface.co/collections/AmazonScience/migrationbench-68125452fc21a4564b92b6c3) Datasets
 
-- It includes both single-job and batch processing capabilities with AWS EMRS support.
+| Index | Dataset                                       | Size  | Notes                                                                                               |
+|-------|-----------------------------------------------|-------|-----------------------------------------------------------------------------------------------------|
+| 1     | [🤗 AmazonScience/migration-bench-java-full](https://huggingface.co/datasets/AmazonScience/migration-bench-java-full)         | 5,102 | Each repo has a test directory or at least one test case                              |
+| 2     | [🤗 AmazonScience/migration-bench-java-selected](https://huggingface.co/datasets/AmazonScience/migration-bench-java-selected) |   300 | A **subset** of migration-bench-java-full                                          |
 
+## 3. Installation
 
-## 📊 Data
+### 3.1 Prerequisites
+
+Verify you have `java 17` and `maven 3.9.6` installed:
+
+```bash
+# java
+$ java --version
+openjdk 17.0.15 2025-04-15 LTS
+OpenJDK Runtime Environment Corretto-17.0.15.6.1 (build 17.0.15+6-LTS)
+OpenJDK 64-Bit Server VM Corretto-17.0.15.6.1 (build 17.0.15+6-LTS, mixed mode, sharing)
+```
+
+```bash
+# maven
+$ mvn --version
+Apache Maven 3.9.6 (bc0240f3c744dd6b6ec2920b3cd08dcc295161ae)
+Maven home: /usr/local/bin/apache-maven-3.9.6
+Java version: 17.0.15, vendor: Amazon.com Inc., runtime: /usr/lib/jvm/java-17-amazon-corretto.x86_64
+```
+If you haven't done it yet, follow the instructions in [MigrationBench](https://github.com/amazon-science/MigrationBench) to install Maven.
+
+### 3.2 Install Package
+
+```bash
+# cd .../JavaMigration/
+
+pip install -r requirements.txt -e .
+```
+
+Or with uv:
+
+```bash
+# cd .../JavaMigration/
+
+uv pip install -e .
+```
+
+## 4. Usage
+
+See the full binary script at [src/java_migration_agent/main.py](https://github.com/amazon-science/JavaMigration/blob/main/src/java_migration_agent/main.py).
+
+
+### 4.1 Agent Types
+
+| Agent Type | Description |
+|------------|-------------|
+| `baseline` | Direct LLM migration with `mvn clean verify` |
+| `pe`       | Baseline with prompt engineering for dependency updates |
+| `rag`      | Uses dependency version lookup tool for migration |
+| `hybrid`   | Pre-processes pom.xml dependencies before LLM migration |
+
+### 4.2 Running Migration
+
+Run batch migration on the MigrationBench dataset:
+
+```bash
+python -m java_migration_agent \
+    --agent-type baseline \
+    --exp-id exp-001 \
+    --hf-dataset AmazonScience/migration-bench-java-selected \
+    --model-id global.anthropic.claude-sonnet-4-5-20250929-v1:0 \
+    --max-workers 8 \
+    --output-dir ./migration_results
+```
+
+### 4.3 Command Line Options
+
+
+| Flag   | Type | Default | Description |
+|--------|------|---------|-------------|
+| `--agent-type` | `str` | (required) | Agent type: `baseline`, `pe`, `rag`, or `hybrid` |
+| `--exp-id` | `str` | (required) | Experiment identifier for organizing results |
+| `--hf-dataset` | `str` | `AmazonScience/migration-bench-java-selected` | HuggingFace dataset name |
+| `--model-id` | `str` | `global.anthropic.claude-sonnet-4-5-20250929-v1:0` | Bedrock model ID |
+| `--temperature` | `float` | `1.0` | Model temperature |
+| `--max-messages` | `int`  | `80` | Maximum messages per conversation |
+| `--max-workers` | `int`  | `8` | Maximum parallel workers |
+| `--output-dir` | `str` | `./migration_results` | Output directory for results |
+
+## 5. 📊 Data
 
 Agent trajectories and execution results are stored in the `data/` folder.
 
-## 🔗 Resources
+## 6. 🔗 Resources
 
 1. 🤗 [MigrationBench (Hugging Face)](https://huggingface.co/collections/AmazonScience/migrationbench-68125452fc21a4564b92b6c3)
 1. 💻 [MigrationBench (GitHub)](https://github.com/amazon-science/MigrationBench)
 1. 📄 [arXiv Paper](https://arxiv.org/abs/2505.09569)
 
 
-## 📚 Citation
+## 7. 📚 Citation
 
 ```bibtex
 @misc{liu2025migrationbenchrepositorylevelcodemigration,