Correct repository clone command and normalize GitHub links to EngiAI-Public

README.demo.md

@@ -32,8 +32,8 @@ Reboot, then open the new Ubuntu terminal and finish the first-run setup.
 
 ```bash
 cd ~
-git clone git@github.com:gioelemo/EngiAI.git
-cd EngiAI
+git clone https://github.com/gioelemo/EngiAI-Public.git
+cd EngiAI-Public
 ```
 
 > **Windows / WSL only:** clone into the WSL filesystem (e.g. `~`), **not** under `/mnt/c/...`. Docker builds are dramatically slower across the Windows/WSL mount boundary and line endings can cause build issues.

README.md

@@ -3,8 +3,8 @@
 </p>
 
 [![Python 3.13](https://img.shields.io/badge/python-3.13-blue.svg)](https://www.python.org/downloads/)
-[![Python tests](https://github.com/gioelemo/EngiAI/actions/workflows/test.yml/badge.svg)](https://github.com/gioelemo/EngiAI/actions/workflows/test.yml)
-[![pre-commit](https://github.com/gioelemo/EngiAI/actions/workflows/pre-commit.yaml/badge.svg)](https://github.com/gioelemo/EngiAI/actions/workflows/pre-commit.yaml)
+[![Python tests](https://github.com/gioelemo/EngiAI-Public/actions/workflows/test.yml/badge.svg)](https://github.com/gioelemo/EngiAI-Public/actions/workflows/test.yml)
+[![pre-commit](https://github.com/gioelemo/EngiAI-Public/actions/workflows/pre-commit.yaml/badge.svg)](https://github.com/gioelemo/EngiAI-Public/actions/workflows/pre-commit.yaml)
 [![Code style: Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff)
 [![Checked with mypy](https://www.mypy-lang.org/static/mypy_badge.svg)](https://mypy-lang.org/)
 
@@ -23,8 +23,8 @@ EngiAI provides an AI-powered assistant for mechanical engineering design, integ
 **Full stack** (Docker):
 
 ```bash
-git clone https://github.com/gioelemo/EngiAI.git
-cd EngiAI
+git clone https://github.com/gioelemo/EngiAI-Public.git
+cd EngiAI-Public
 cp .env.example .env       # add OPENAI_API_KEY / GOOGLE_API_KEY / TAVILY_API_KEY
 docker compose up -d
 ```
@@ -82,5 +82,5 @@ tests/        # unit and integration tests
 ## Getting help
 
 - [Troubleshooting guide](docs/source/troubleshooting.md)
-- [GitHub Issues](https://github.com/gioelemo/EngiAI/issues)
+- [GitHub Issues](https://github.com/gioelemo/EngiAI-Public/issues)
 - Container logs: `docker compose logs -f`

benchmarks/README.md

@@ -468,10 +468,13 @@ This is helpful for diagnosing issues and understanding agent behavior.
 If you use these benchmarks in your research, please cite:
 
 ```bibtex
-@software{engiai_benchmarks,
-  title = {EngiAI Benchmarks},
-  author = {Your Name},
-  year = {2024},
-  url = {https://github.com/gioelemo/EngiAI}
+@misc{molinari2026engiaimultiagentframeworkbenchmark,
+      title={EngiAI: A Multi-Agent Framework and Benchmark Suite for LLM-Driven Engineering Design}, 
+      author={Gioele Molinari and Florian Felten and Soheyl Massoudi and Mark Fuge},
+      year={2026},
+      eprint={2605.19743},
+      archivePrefix={arXiv},
+      primaryClass={cs.AI},
+      url={https://arxiv.org/abs/2605.19743}, 
 }
 ```

docs/source/conf.py

@@ -77,7 +77,7 @@
 
 # Theme options - matching EngiBench style
 html_theme_options = {
-    "repository_url": "https://github.com/gioelemo/EngiAI",
+    "repository_url": "https://github.com/gioelemo/EngiAI-Public",
     "repository_branch": "main",
     "path_to_docs": "docs/",
     "use_repository_button": True,

docs/source/contributing.md

@@ -8,7 +8,7 @@ Thank you for your interest in contributing to EngiAI! This document provides gu
 2. **Clone your fork**:
    ```bash
    git clone https://github.com/YOUR_USERNAME/engiai.git
-   cd EngiAI
+   cd EngiAI-Public
    ```
 3. **Create environment and install dependencies**:
    ```bash
@@ -291,8 +291,8 @@ Your PR should:
 
 ## Questions?
 
-- Open an [issue](https://github.com/gioelemo/EngiAI/issues) for bugs
-- Start a [discussion](https://github.com/gioelemo/EngiAI/discussions) for questions
+- Open an [issue](https://github.com/gioelemo/EngiAI-Public/issues) for bugs
+- Start a [discussion](https://github.com/gioelemo/EngiAI-Public/discussions) for questions
 - Join our community chat (if available)
 
 ## License

docs/source/deployment.md

@@ -75,7 +75,7 @@ unzip engiai-v1.0.0.zip -d engiai
 unzip prusa-mcp-server-v1.0.0.zip -d .
 
 # Navigate to the application directory
-cd EngiAI
+cd EngiAI-Public
 ```
 
 ### Step 3: Configure Environment Variables
@@ -424,7 +424,7 @@ crontab -e
 ## Support
 
 For issues and support:
-- GitHub Issues: https://github.com/gioelemo/EngiAI/issues
+- GitHub Issues: https://github.com/gioelemo/EngiAI-Public/issues
 - Documentation: https://gioelemo.github.io/EngiAI/
 
 ## Version

docs/source/index.rst

@@ -157,15 +157,14 @@ Getting Help
 ============
 
 * **Troubleshooting**: See :doc:`troubleshooting` for common issues
-* **GitHub Issues**: `Report bugs or request features <https://github.com/gioelemo/EngiAI/issues>`_
+* **GitHub Issues**: `Report bugs or request features <https://github.com/gioelemo/EngiAI-Public/issues>`_
 * **Documentation**: Browse the guides in the sidebar
 * **Examples**: Check the ``scripts/`` directory in the repository
 
 Project Links
 =============
 
-* **GitHub**: https://github.com/gioelemo/EngiAI
-* **Documentation**: https://gioelemo.github.io/EngiAI/
+* **GitHub**: https://github.com/gioelemo/EngiAI-Public
 * **License**: MIT
 
 Indices and tables

docs/source/installation.md

@@ -39,8 +39,8 @@ See `services/prusa_mcp_server/README.md` for details.
 #### 2. Clone the Repository
 
 ```bash
-git clone https://github.com/gioelemo/EngiAI.git
-cd EngiAI
+git clone https://github.com/gioelemo/EngiAI-Public.git
+cd EngiAI-Public
 ```
 
 #### 3. Configure Environment
@@ -119,7 +119,7 @@ For developers who want to modify the code or run without Docker.
 
 **First, navigate to the project directory:**
 ```bash
-cd EngiAI
+cd EngiAI-Public
 ```
 
 **Then follow the manual installation steps below.** Automated setup scripts are not currently provided.
@@ -129,8 +129,8 @@ cd EngiAI
 #### Step 1: Clone the Repository
 
 ```bash
-git clone https://github.com/gioelemo/EngiAI.git
-cd EngiAI
+git clone https://github.com/gioelemo/EngiAI-Public.git
+cd EngiAI-Public
 ```
 
 #### Step 2: Create Conda Environment
@@ -280,7 +280,7 @@ If pre-commit hooks are causing issues:
 If you encounter issues not covered here:
 
 1. Check [Troubleshooting Guide](troubleshooting.md)
-2. Check existing [GitHub Issues](https://github.com/gioelemo/EngiAI/issues)
+2. Check existing [GitHub Issues](https://github.com/gioelemo/EngiAI-Public/issues)
 3. Open a new issue with:
    - Your operating system
    - Python version (`python --version`) or Docker version

docs/source/quickstart.md

@@ -25,8 +25,8 @@ The easiest and most reliable way to get started:
 ### 1. Clone and Navigate
 
 ```bash
-git clone https://github.com/gioelemo/EngiAI.git
-cd EngiAI
+git clone https://github.com/gioelemo/EngiAI-Public.git
+cd EngiAI-Public
 ```
 
 ### 2. Configure Environment
@@ -195,5 +195,5 @@ This allows the containerized assistant to:
 ## Need Help?
 
 - [Troubleshooting Guide](troubleshooting.md)
-- [GitHub Issues](https://github.com/gioelemo/EngiAI/issues)
+- [GitHub Issues](https://github.com/gioelemo/EngiAI-Public/issues)
 - Check the `scripts/` directory for code examples

docs/source/troubleshooting.md

@@ -543,7 +543,7 @@ If your issue isn't covered here:
    tail -f data/*.log
    ```
 
-2. **Search GitHub Issues**: https://github.com/gioelemo/EngiAI/issues
+2. **Search GitHub Issues**: https://github.com/gioelemo/EngiAI-Public/issues
 
 3. **Open a new issue** with:
    - Operating system

docs/source/usage/prusa.md

@@ -375,7 +375,7 @@ ls -lh outputs/*.stl
 ## Further Reading
 
 - [Prusa Connect Documentation](https://help.prusa3d.com/guide/prusa-connect_245530)
-- [MCP Server Code](https://github.com/gioelemo/EngiAI/tree/main/services/prusa_mcp_server)
+- [MCP Server Code](https://github.com/gioelemo/EngiAI-Public/tree/main/services/prusa_mcp_server)
 - [Docker Deployment](../docker_deployment.md)
 - [Architecture Overview](../architecture.md)
 

docs/source/weave_integration.md

@@ -42,8 +42,8 @@ python evaluate_agent.py \
 ```
 
 **📚 For complete documentation see:**
-- [**Benchmarks Overview**](https://github.com/gioelemo/EngiAI/blob/main/benchmarks/README.md) - Available problems, datasets, and metrics
-- [**Evaluation Guide**](https://github.com/gioelemo/EngiAI/blob/main/benchmarks/evaluations/README.md) - How to run evaluations and configure scorers
+- [**Benchmarks Overview**](https://github.com/gioelemo/EngiAI-Public/blob/main/benchmarks/README.md) - Available problems, datasets, and metrics
+- [**Evaluation Guide**](https://github.com/gioelemo/EngiAI-Public/blob/main/benchmarks/evaluations/README.md) - How to run evaluations and configure scorers
 
 ### Available Problem Types
 
@@ -55,7 +55,7 @@ Three engineering optimization problems are available:
 | **photonics2d** | 120×120 grids | Photonic devices | Transmission efficiency, volume |
 | **thermoelastic2d** | Variable size | Thermal structures | Compliance, thermal loss, volume |
 
-See [benchmarks/README.md](https://github.com/gioelemo/EngiAI/blob/main/benchmarks/README.md) for detailed problem descriptions.
+See [benchmarks/README.md](https://github.com/gioelemo/EngiAI-Public/blob/main/benchmarks/README.md) for detailed problem descriptions.
 
 ## Evaluation Workflow
 
@@ -103,7 +103,7 @@ python evaluate_agent.py --problem beams2d --scorers all
 python evaluate_agent.py --problem beams2d --scorers task_completion
 ```
 
-See the [Evaluation Guide](https://github.com/gioelemo/EngiAI/blob/main/benchmarks/evaluations/README.md) for scorer details.
+See the [Evaluation Guide](https://github.com/gioelemo/EngiAI-Public/blob/main/benchmarks/evaluations/README.md) for scorer details.
 
 ### 4. View Results
 
@@ -140,7 +140,7 @@ as a Weave scorer — they are computed offline by
 - **RVC (Ratio of Violated Constraints)**: Fraction of designs violating constraints (lower is better)
 - **Optimality Gap (IOG/COG/FOG)**: Distance from optimal solutions
 
-See [benchmarks/README.md](https://github.com/gioelemo/EngiAI/blob/main/benchmarks/README.md#metrics) for detailed metric definitions.
+See [benchmarks/README.md](https://github.com/gioelemo/EngiAI-Public/blob/main/benchmarks/README.md#metrics) for detailed metric definitions.
 
 ## Advanced Usage
 
@@ -202,7 +202,7 @@ To add a new optimization problem to the benchmark suite:
 3. **Implement generator**: Create `generate_prompts.py` for your problem
 4. **Add dataset**: Create or reference HuggingFace dataset
 
-See the [Evaluation Guide](https://github.com/gioelemo/EngiAI/blob/main/benchmarks/evaluations/README.md#adding-new-problem-types) for complete instructions.
+See the [Evaluation Guide](https://github.com/gioelemo/EngiAI-Public/blob/main/benchmarks/evaluations/README.md#adding-new-problem-types) for complete instructions.
 
 ## Best Practices
 
@@ -270,9 +270,9 @@ python evaluate_agent.py --problem beams2d --scorers custom  # Not supported
 
 ## Further Reading
 
-- [Benchmarks Overview](https://github.com/gioelemo/EngiAI/blob/main/benchmarks/README.md) - Complete benchmark system documentation
-- [Evaluation Guide](https://github.com/gioelemo/EngiAI/blob/main/benchmarks/evaluations/README.md) - Detailed evaluation instructions
-- [Problem Registry](https://github.com/gioelemo/EngiAI/blob/main/benchmarks/shared/problem_registry.py) - Problem configuration reference
+- [Benchmarks Overview](https://github.com/gioelemo/EngiAI-Public/blob/main/benchmarks/README.md) - Complete benchmark system documentation
+- [Evaluation Guide](https://github.com/gioelemo/EngiAI-Public/blob/main/benchmarks/evaluations/README.md) - Detailed evaluation instructions
+- [Problem Registry](https://github.com/gioelemo/EngiAI-Public/blob/main/benchmarks/shared/problem_registry.py) - Problem configuration reference
 - [Weave Documentation](https://docs.wandb.ai/weave) - Official Weave documentation
 
 ## Technical Integration Details
@@ -326,4 +326,4 @@ else:
     print("Weave disabled, using local logging")
 ```
 
-See [Weave Integration Utils](https://github.com/gioelemo/EngiAI/blob/main/src/utils/weave_integration.py) for implementation details.
+See [Weave Integration Utils](https://github.com/gioelemo/EngiAI-Public/blob/main/src/utils/weave_integration.py) for implementation details.