diff --git a/.github/copilot-instructions.md b/.github/copilot-instructions.md
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+# CodeQL Development Toolkit (QLT)
+
+Always reference these instructions first and fallback to search or bash commands only when you encounter unexpected information that does not match the info here.
+
+## Working Effectively
+
+### Prerequisites and Installation
+- Install .NET 6.0 SDK for development and testing:
+  ```bash
+  wget https://dot.net/v1/dotnet-install.sh -O dotnet-install.sh
+  chmod +x dotnet-install.sh
+  ./dotnet-install.sh --channel 6.0
+  export PATH="$HOME/.dotnet:$PATH"
+  ```
+- The project requires .NET 6.0 runtime for execution, but can be built with .NET 8.0.
+- For production use, download pre-built releases from GitHub releases page (Linux x86_64 only).
+
+### Bootstrap, Build, and Test
+- **Restore dependencies**: `dotnet restore` -- takes 20 seconds. NEVER CANCEL. Set timeout to 60+ seconds.
+- **Build the project**: `dotnet build -c Release --no-restore` -- takes 9 seconds. NEVER CANCEL. Set timeout to 30+ seconds.
+- **Run tests**: `dotnet test -c Release --no-build` -- takes 3 seconds. Set timeout to 15+ seconds.
+- **Note**: Tests require .NET 6.0 runtime. Build will complete with warnings (nullable reference types) but no errors.
+
+### Run the Application
+- **During development**: `dotnet run --project src/CodeQLToolkit.Core --configuration Release -- [command]`
+- **From published binary**: `dotnet publish src/CodeQLToolkit.Core/CodeQLToolkit.Core.csproj -c Release -o publish-out` then use `./publish-out/CodeQLToolkit.Core [command]`
+- **Self-contained build**: `dotnet publish src/CodeQLToolkit.Core/CodeQLToolkit.Core.csproj -c Release -o publish-standalone --self-contained -r linux-x64` -- takes 4 seconds. Creates standalone executable.
+
+### Basic Application Commands
+- **Get help**: `qlt --help` or add `--help` to any command
+- **Get version**: `qlt version`
+- **Initialize query development**: `qlt query init --automation-type actions`
+- **Set CodeQL version**: `qlt codeql set version --automation-type actions` (creates `qlt.conf.json`)
+- **Initialize testing**: `qlt test init --language [c|cpp|csharp|go|java|javascript|python|ruby] --automation-type actions`
+  - Creates `.github/workflows/run-codeql-unit-tests-[language].yml`
+  - Creates `.github/actions/install-qlt/action.yml`
+  - Example: `qlt test init --language cpp --automation-type actions`
+
+## Validation
+
+### Always Run Before Committing
+- Build the project: `dotnet build -c Release`
+- Run tests: `dotnet test -c Release`
+- The build produces 151 warnings (nullable reference types) but no errors - this is expected.
+
+### Manual Validation Scenarios
+After making changes, always test key functionality:
+1. **Basic functionality**: Run `qlt version` and `qlt --help` to ensure the application starts correctly.
+2. **Repository initialization**: 
+   - Create a test directory: `mkdir /tmp/qlt-test && cd /tmp/qlt-test`
+   - Run: `qlt query init --automation-type actions`
+   - Verify `codeql-workspace.yml` is created
+   - Run: `qlt codeql set version --automation-type actions`
+   - Verify `qlt.conf.json` is created with expected structure
+   - Run: `qlt test init --language cpp --automation-type actions`
+   - Verify GitHub Actions workflows are created in `.github/workflows/` and `.github/actions/`
+3. **Help system**: Test help for main commands: `qlt query --help`, `qlt test --help`, `qlt codeql --help`
+4. **Commands requiring CodeQL**: Note that validation commands like `qlt validation run check-queries` require CodeQL to be installed and will fail with "CodeQL not installed" if not available. This is expected behavior.
+
+### CI/CD Validation
+- The project uses GitHub Actions for CI/CD with workflows in `.github/workflows/`
+- Build artifacts are created as zip files for distribution
+- No specific linting tools beyond standard .NET compiler warnings
+
+## Common Tasks
+
+### Repository Structure
+QLT expects CodeQL repositories to follow this structure:
+```
+Repo Root
+│   codeql-workspace.yml
+│   qlt.conf.json
+│
+└───[language] (e.g., cpp, java, javascript)
+    ├───[package-name]
+    │   ├───src
+    │   │   │   qlpack.yml
+    │   │   └───[QueryName]
+    │   │           QueryName.ql
+    │   └───test
+    │       │   qlpack.yml
+    │       └───[QueryName]
+    │               TestFile.cpp
+    │               TestFile.expected
+    │               TestFile.qlref
+```
+
+### Key Features
+- **Query Management**: Create, scaffold, and manage CodeQL queries
+- **Unit Testing**: Run and validate CodeQL unit tests in parallel
+- **CI/CD Integration**: Generate GitHub Actions workflows for automated testing
+- **Validation**: Check query metadata and structure
+- **Pack Management**: Manage CodeQL packs and dependencies
+- **Bundle Creation**: Create custom CodeQL bundles for distribution
+
+### Example Workflows
+- **Create new query repository**: `qlt query init && qlt codeql set version`
+- **Setup CI/CD for C++ queries**: `qlt test init --language cpp --automation-type actions`
+- **Run unit tests locally**: `qlt test run execute-unit-tests --num-threads 4 --language cpp --runner-os "Linux" --work-dir /tmp/test-results`
+- **Validate queries**: `qlt validation run check-queries --language cpp --pretty-print`
+
+## Development Tips
+- The application is organized into **Features** with lifecycle and command components
+- Source code is in `src/` with three main projects: Core, Features, and Shared
+- Templates for code generation are in the `Templates/` directory
+- The `example/` directory contains sample CodeQL repository structures
+- Build produces warnings about nullable reference types - this is expected and should not be "fixed"
+- Use `--base` parameter to specify working directory (defaults to current directory)
+- Always use `--automation-type actions` for GitHub Actions integration
+
+## Important Files
+- `src/CodeQLToolkit.Core/` - Main executable project
+- `src/CodeQLToolkit.Features/` - Core functionality and commands
+- `src/CodeQLToolkit.Shared/` - Shared utilities and base classes
+- `CodeQLToolkit.sln` - Visual Studio solution file
+- `.github/workflows/` - CI/CD pipeline definitions
+- `scripts/` - Build and release automation scripts
+- `example/` - Sample repository structures and configurations
\ No newline at end of file
diff --git a/.gitignore b/.gitignore
index 3c0b66a..8126887 100644
--- a/.gitignore
+++ b/.gitignore
@@ -362,3 +362,8 @@ MigrationBackup/
 # Fody - auto-generated XML schema
 FodyWeavers.xsd
 /dist/
+
+# Custom build artifacts
+publish-out/
+publish-out-standalone/
+dotnet-install.sh