diff --git a/.github/workflows/colab.yml b/.github/workflows/colab.yml
index 7946adfd5d..4ece61ca6a 100644
--- a/.github/workflows/colab.yml
+++ b/.github/workflows/colab.yml
@@ -16,7 +16,7 @@ on:
 
 jobs:
   colab:
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-latest
     env:
         COLAB_ALWAYS_INSTALL_XVFB: 1
         QLEARNING_NUM_TRAINING_STEPS: 5
diff --git a/.github/workflows/pre-commit.yml b/.github/workflows/pre-commit.yml
index d1422573e8..1a77b13354 100644
--- a/.github/workflows/pre-commit.yml
+++ b/.github/workflows/pre-commit.yml
@@ -13,7 +13,11 @@ jobs:
   pre-commit:
     runs-on: ubuntu-24.04
     env:
-        DOTNET_NOLOGO: 1
+      DOTNET_NOLOGO: 1
+      DOTNET_SKIP_FIRST_TIME_EXPERIENCE: "1"
+      DOTNET_CLI_HOME: "${{ github.workspace }}/.dotnet"
+      NUGET_PACKAGES: "${{ github.workspace }}/.nuget/packages"
+      TMPDIR: "${{ github.workspace }}/.tmp"
     steps:
     - uses: actions/checkout@v4
     - uses: actions/setup-python@v5
@@ -25,15 +29,20 @@ jobs:
       with:
         ruby-version: '2.7'
         bundler-cache: true # runs 'bundle install' and caches installed gems automatically
+    - name: Create writable dirs
+      run: |
+        mkdir -p "$DOTNET_CLI_HOME" "$NUGET_PACKAGES" "$TMPDIR"
     - uses: actions/setup-dotnet@v4
       with:
         dotnet-version: '8.0.202'
-    -   name: Clean dotnet shared memory
-        run: sudo rm -rf /tmp/.dotnet/shm
     - name: Install manual dependencies
       run: |
         python -m pip install pre-commit
         pre-commit install
+    - name: Pre-warm dotnet
+      run: |
+        dotnet --info
+        dotnet restore || true
     - name: Run pre-commit
       run: |
         pre-commit run --all-files
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 08a8e33e72..2ab764c102 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -94,7 +94,8 @@ repos:
     -   id: dotnet-format
         name: dotnet-format
         language: system
-        entry: dotnet format whitespace --folder --include
+        entry: dotnet format whitespace --folder --include . --verify-no-changes
+        pass_filenames: false
         types_or: ["c#"]
     -   id: markdown-link-check
         name: markdown-link-check
diff --git a/.yamato/com.unity.ml-agents-test.yml b/.yamato/com.unity.ml-agents-test.yml
index 6a62b4b85c..dc0aeca828 100644
--- a/.yamato/com.unity.ml-agents-test.yml
+++ b/.yamato/com.unity.ml-agents-test.yml
@@ -8,7 +8,7 @@ test_editors:
       enableNoDefaultPackages: !!bool true
 
 trunk_editor:
-    - version: trunk
+    - version: 6000.4
       testProject: DevProject
 
 test_platforms:
diff --git a/.yamato/test_versions.metafile b/.yamato/test_versions.metafile
index abcec74931..2d4a1ee5d3 100644
--- a/.yamato/test_versions.metafile
+++ b/.yamato/test_versions.metafile
@@ -7,5 +7,5 @@ test_editors:
     extra_test: gym
   - version: 6000.0
     extra_test: sensor
-  - version: trunk
+  - version: 6000.3
     extra_test: llapi
diff --git a/CLAUDE.md b/CLAUDE.md
new file mode 100644
index 0000000000..f4c88f2094
--- /dev/null
+++ b/CLAUDE.md
@@ -0,0 +1,178 @@
+# CLAUDE.md
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+
+## Project Overview
+
+The Unity ML-Agents Toolkit is a sophisticated machine learning infrastructure project that bridges Unity game development (C#) with Python-based ML training. It enables games and simulations to serve as environments for training intelligent agents using reinforcement learning, imitation learning, and other ML techniques.
+
+This is a **monorepo** with multiple interconnected packages:
+- `com.unity.ml-agents/` - Unity Package (C# SDK)
+- `ml-agents/` - Python Trainer Package
+- `ml-agents-envs/` - Python Environment Interface
+- `ml-agents-trainer-plugin/` - Plugin framework
+- `protobuf-definitions/` - Communication protocol definitions
+- `config/` - Training configuration examples
+- `Project/` and `DevProject/` - Example Unity projects
+
+## Common Development Commands
+
+### Python Package Installation (Development Mode)
+```bash
+# Install packages in editable mode for development
+pip install -e ./ml-agents-envs
+pip install -e ./ml-agents
+pip install -e ./ml-agents-trainer-plugin
+pip install -e ./ml-agents-plugin-examples
+
+# Install test dependencies
+pip install -r test_requirements.txt
+```
+
+### Testing
+```bash
+# Run all tests except slow ones (default for development)
+pytest -m "not slow"
+
+# Run tests with parallel execution (8 workers)
+pytest -m "not slow" -n 8
+
+# Run tests with coverage reporting
+pytest --cov=ml-agents --cov=ml-agents-envs --cov-report html
+
+# Run slow tests (training-related, takes much longer)
+pytest -m slow
+
+# Run specific test file
+pytest ml-agents/mlagents/trainers/tests/test_buffer.py
+
+# Run specific test function
+pytest ml-agents/mlagents/trainers/tests/test_buffer.py::test_buffer_functionality
+```
+
+### Code Quality and Formatting
+```bash
+# Run pre-commit hooks on all files
+pre-commit run --all-files
+
+# Run specific hooks
+pre-commit run black --all-files
+pre-commit run mypy --all-files
+pre-commit run flake8 --all-files
+
+# Format C# code
+dotnet format whitespace --folder --include
+
+# Check markdown links (manual stage)
+pre-commit run --hook-stage manual markdown-link-check
+```
+
+### Training Commands
+```bash
+# Basic training command
+mlagents-learn config/ppo/3DBall.yaml --env=Project/3DBall --run-id=my_run
+
+# Training with curriculum learning
+mlagents-learn config/curricula/Wall.yaml --env=Project/WallJump --run-id=wall_curriculum
+
+# Resume training from checkpoint
+mlagents-learn config/ppo/3DBall.yaml --env=Project/3DBall --run-id=my_run --resume
+
+# Push trained model to Hugging Face
+mlagents-push-to-hf --run-id=my_run --repo-name=my-org/my-model
+```
+
+### Building and Unity Integration
+```bash
+# Unity Package Manager operations (from Unity Editor)
+# Window > Package Manager > + > Add package from git URL
+# https://github.com/Unity-Technologies/ml-agents.git?path=com.unity.ml-agents
+
+# Build Unity project (from Unity Editor or command line)
+Unity -batchmode -quit -projectPath ./Project -buildTarget StandaloneLinux64
+```
+
+## Architecture Overview
+
+### Communication Flow
+The system uses a **gRPC-based architecture**:
+```
+Unity Environment ←→ gRPC ←→ Python Trainer
+    (C# SDK)                    (PyTorch/ML)
+```
+
+### Key Components
+
+**Python Side:**
+- **Trainers** (`ml-agents/mlagents/trainers/`): Core ML algorithms (PPO, SAC, MA-POCA, GAIL, BC)
+- **Environment Interface** (`ml-agents-envs/`): Communication with Unity environments
+- **Plugin System**: Extensible trainer types and stats writers via entry points
+
+**Unity Side:**
+- **Agent** (`com.unity.ml-agents/Runtime/Agent.cs`): Base class for trainable agents
+- **Sensors**: Observation collection (vision, raycast, grid sensors)
+- **Actuators**: Action execution (continuous/discrete)
+- **Communicator**: gRPC communication layer
+
+### Multi-Package Structure
+
+The project uses **separate Python packages** with careful version management:
+- Packages can be installed independently
+- Version constraints are strictly managed (see `setup.py` files)
+- Plugin system uses entry points for extensibility
+
+## Development Workflow
+
+### Code Quality Standards
+- **Python**: Black formatting (120 char line length), mypy type checking, flake8 linting
+- **C#**: dotnet-format for whitespace formatting
+- **Testing**: pytest with 60% minimum coverage requirement
+- **Pre-commit hooks**: Enforced via `.pre-commit-config.yaml`
+
+### Important Constraints
+- **Python Version**: 3.10.1-3.10.12 only
+- **PyTorch**: ≤2.8.0 (strict constraint to prevent ONNX breaking changes)
+- **Unity**: 6000.0+ (Unity 6)
+- **Banned modules**: Direct tensorflow/torch imports (use utils instead)
+
+### Testing Strategy
+- **Parallel execution**: Tests run with 8 workers using pytest-xdist
+- **Port allocation**: Custom `base_port` fixture prevents port collisions
+- **Slow tests**: Training-related tests marked with `@pytest.mark.slow`
+- **Coverage**: HTML reports available via `--cov-report html`
+
+### Plugin Development
+Extend functionality via entry points in `setup.py`:
+```python
+entry_points={
+    ML_AGENTS_STATS_WRITER: ["custom_writer=my_package:MyStatsWriter"],
+    ML_AGENTS_TRAINER_TYPE: ["custom_trainer=my_package:MyTrainer"]
+}
+```
+
+## Key Files for Development
+
+**Configuration:**
+- `config/` - Training configuration YAML files for different algorithms
+- `.pre-commit-config.yaml` - Code quality enforcement
+- `pytest.ini`, `setup.cfg` - Test and coverage configuration
+
+**Architecture Entry Points:**
+- `ml-agents/mlagents/trainers/learn.py` - Main training script
+- `ml-agents-envs/mlagents_envs/environment.py` - Environment interface
+- `com.unity.ml-agents/Runtime/Agent.cs` - Unity agent base class
+
+**Documentation:**
+- Primary docs: [Unity Package Documentation](https://docs.unity3d.com/Packages/com.unity.ml-agents@latest)
+- Legacy docs: `docs/` directory (deprecated)
+
+## Release and Versioning
+
+- **Main branch**: `develop` (unstable development)
+- **Release branch pattern**: `release_XX`
+- **Version validation**: Pre-commit hooks ensure version consistency across packages
+- **Git tags**: Must match `__release_tag__` in `__init__.py` files
+
+## Port Management
+
+Tests use a **file-lock based port allocation system** (`conftest.py`) to enable parallel execution without port conflicts. Ports are dynamically allocated starting from a base port calculated per test file.
\ No newline at end of file
diff --git a/colab/Colab_UnityEnvironment_1_Run.ipynb b/colab/Colab_UnityEnvironment_1_Run.ipynb
index e70dca7b8a..9ac80f920f 100644
--- a/colab/Colab_UnityEnvironment_1_Run.ipynb
+++ b/colab/Colab_UnityEnvironment_1_Run.ipynb
@@ -217,7 +217,7 @@
     "\n",
     "from mlagents_envs.registry import default_registry\n",
     "\n",
-    "env = default_registry[env_id].make()"
+    "env = default_registry[env_id].make(no_graphics=True)"
    ],
    "execution_count": 3,
    "outputs": [
diff --git a/com.unity.ml-agents/CHANGELOG.md b/com.unity.ml-agents/CHANGELOG.md
index d0b4d9dd15..a2b7b7d1fb 100755
--- a/com.unity.ml-agents/CHANGELOG.md
+++ b/com.unity.ml-agents/CHANGELOG.md
@@ -6,11 +6,12 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to
 [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
-## [Unreleased]
+## [4.0.1] - 2025-12-04
 ### Minor Changes
 #### com.unity.ml-agents (C#)
 - Fixed tensor indexing to use correct CHW layout (#6239)
 - Updated the installation doc (#6242)
+- Fixed Unity Editor crashing when quitting in play mode (#6267)
 
 #### ml-agents / ml-agents-envs
 - Set the Torch version constraint to 2.8 (#6251)
diff --git a/com.unity.ml-agents/Documentation~/Reference-Support.md b/com.unity.ml-agents/Documentation~/Reference-Support.md
index 922e65c79d..8c891229f9 100644
--- a/com.unity.ml-agents/Documentation~/Reference-Support.md
+++ b/com.unity.ml-agents/Documentation~/Reference-Support.md
@@ -3,10 +3,11 @@
 The Reference & Support section contains essential documentation for ongoing ML-Agents development.
 
 
-| **Resource**                         | **Description**                                              |
-|--------------------------------------|--------------------------------------------------------------|
-| [FAQ](FAQ.md)                        | Frequently asked questions and common issues with solutions. |
-| [Limitations](Limitations.md)        | Known limitations and constraints of the ML-Agents Toolkit.  |
-| [Migrating](Migrating.md)            | Migration guides for updating between ML-Agents versions.    |
-| [Versioning](Versioning.md)          | Information about ML-Agents versioning and release notes.    |
-| [ML-Agents Glossary](Glossary.md)    | Glossary of terms and concepts used in ML-Agents.            |
+| **Resource**                               | **Description**                                              |
+|--------------------------------------------|--------------------------------------------------------------|
+| [FAQ](FAQ.md)                              | Frequently asked questions and common issues with solutions. |
+| [Limitations](Limitations.md)              | Known limitations and constraints of the ML-Agents Toolkit.  |
+| [Migrating](Migrating.md)                  | Migration guides for updating between ML-Agents versions.    |
+| [Versioning](Versioning.md)                | Information about ML-Agents versioning and release notes.    |
+| [ML-Agents Glossary](Glossary.md)          | Glossary of terms and concepts used in ML-Agents.            |
+| [Contribution guidelines](CONTRIBUTING.md) | How to Contribute to ML-Agents.                              |
diff --git a/com.unity.ml-agents/Runtime/Academy.cs b/com.unity.ml-agents/Runtime/Academy.cs
index 3cdc15f64c..9957e91f43 100644
--- a/com.unity.ml-agents/Runtime/Academy.cs
+++ b/com.unity.ml-agents/Runtime/Academy.cs
@@ -107,7 +107,7 @@ public class Academy : IDisposable
         /// Unity package version of com.unity.ml-agents.
         /// This must match the version string in package.json and is checked in a unit test.
         /// </summary>
-        internal const string k_PackageVersion = "4.0.0";
+        internal const string k_PackageVersion = "4.0.1";
 
         const int k_EditorTrainingPort = 5004;
 
@@ -261,6 +261,7 @@ protected Academy()
             LazyInitialize();
 
 #if UNITY_EDITOR
+            EditorApplication.quitting += Dispose;
             EditorApplication.playModeStateChanged += HandleOnPlayModeChanged;
 #endif
         }
diff --git a/com.unity.ml-agents/package.json b/com.unity.ml-agents/package.json
index 394fd72689..7467cb4ac8 100755
--- a/com.unity.ml-agents/package.json
+++ b/com.unity.ml-agents/package.json
@@ -1,7 +1,7 @@
 {
   "name": "com.unity.ml-agents",
   "displayName": "ML Agents",
-  "version": "4.0.0",
+  "version": "4.0.1",
   "unity": "6000.0",
   "description": "Use state-of-the-art machine learning to create intelligent character behaviors in any Unity environment (games, robotics, film, etc.).",
   "dependencies": {
diff --git a/ml-agents-envs/mlagents_envs/registry/unity_env_registry.py b/ml-agents-envs/mlagents_envs/registry/unity_env_registry.py
index 896c71ac94..6542d2f441 100644
--- a/ml-agents-envs/mlagents_envs/registry/unity_env_registry.py
+++ b/ml-agents-envs/mlagents_envs/registry/unity_env_registry.py
@@ -121,6 +121,6 @@ def __iter__(self) -> Iterator[Any]:
 
 default_registry = UnityEnvRegistry()
 # TODO restore when a new registry is available.
-default_registry.register_from_yaml(
-    "https://storage.googleapis.com/mlagents-test-environments/1.1.0/manifest.yaml"
-)  # noqa E501
+# default_registry.register_from_yaml(
+#    "https://storage.googleapis.com/mlagents-test-environments/1.1.0/manifest.yaml"
+# )  # noqa E501