AI-Assisted Development Setup

This guide helps Skyline developers configure AI tooling for their development workflow.

Our Recommended Toolset

The Skyline team has standardized on Claude Code for AI-assisted development, similar to how we standardize on ReSharper for code analysis. This provides:

• Consistent workflows across the team
• Shared skills and commands
• Integration with our MCP servers (LabKey, Status)
• Documentation optimized for Claude Code patterns

External contributors are welcome to use other tools (Cursor, VS Code + Copilot, etc.)—the codebase works with any IDE. However, some team-specific tooling (MCP servers, slash commands) is Claude Code-specific.

Complete Setup

Option A: New Machine

Follow the NewMachineBootstrap guide to install Git and Claude Code, then let Claude Code guide you through the rest.

Option B: Existing Development Machine

If you already have a working Skyline build environment (via HowToBuildSkylineTip), you can add AI tooling by installing Claude Code and letting it configure the rest.

Open a PowerShell terminal (not "cmd"):

• Press <kbd>Win</kbd>+<kbd>X</kbd>, then press <kbd>I</kbd> — this opens Terminal (Windows 11) or Windows PowerShell (Windows 10)
• Or search for "PowerShell" in the Start menu

Install Claude Code:

irm https://claude.ai/install.ps1 | iex

If claude isn't recognized after install, add it to PATH:

$claudePath = "$env:USERPROFILE\.local\bin"
[Environment]::SetEnvironmentVariable("Path", [Environment]::GetEnvironmentVariable("Path", "User") + ";$claudePath", "User")

Close and reopen your terminal, then start Claude Code:

cd C:\proj    # or wherever your pwiz checkout is
claude

Once authenticated, paste this prompt:

Help me configure AI tooling for Skyline development.

Use curl (Bash tool) to download this file, then read and follow the instructions:
https://raw.githubusercontent.com/ProteoWizard/pwiz-ai/master/docs/new-machine-setup.md

This is an EXISTING development machine - I already have Visual Studio, Git, and a working Skyline build environment.

Check each component and only install what's missing.

Note that there's an assumption that you have a copy of master checked out at c:\proj\pwiz. That's pretty standard for the team, but if that's not how you work - for example if you work under d:\dev and you keep master in a folder d:\dev\master_clean - then add something like this to the prompt:

Note that I work in D:\dev, not C:\proj - and when I check out master, I put it in D:\dev\master_clean, not D:\dev\pwiz

Enter the prompt and Claude Code will check your environment and add only what's needed.

Keep in mind that you aren't just running a simple script, so if things start to go sideways (e.g. Claude can't find python, or forgets the URL for pwiz-ai repo etc) just have a conversation with Claude and the two of you will get back on track eventually.

Option C: Quick Verification

If you have the AI tooling repository cloned, verify your environment:

pwsh -Command "& './ai/scripts/Verify-Environment.ps1'"

Any [MISSING] items will show the command needed to fix them.

Using Other AI Tools

If you prefer Cursor, VS Code + Copilot, or another AI-assisted IDE:

What Works Everywhere

• All Skyline code, tests, and documentation
• Build scripts in ai/scripts/Skyline/
• Style guide: ai/STYLEGUIDE.md
• Critical rules: ai/CRITICAL-RULES.md

Claude Code-Specific Features

These require Claude Code and won't work in other tools:

• Slash commands (/pw-daily, /pw-commit, etc.)
• Skills (context-loading prompts)
• MCP servers (LabKey, Status, Gmail integration)
• Statusline (custom status display)

Generic Prompt for Other Tools

For Cursor, Copilot Chat, or similar tools, use this prompt to load context:

You are working on the Skyline mass spectrometry application (C#/.NET).

Before making changes, read these files:
- ai/CRITICAL-RULES.md - Absolute constraints (NO async/await, resource strings, etc.)
- ai/STYLEGUIDE.md - Coding conventions
- ai/MEMORY.md - Project context and gotchas

Build with: pwsh -Command "& './ai/scripts/Skyline/Build-Skyline.ps1'"
Test with: pwsh -Command "& './ai/scripts/Skyline/Run-Tests.ps1' -TestName <TestName>"

IDE-Specific Configuration

VS Code / Cursor Terminal Settings

Add to .vscode/settings.json:

{
  "terminal.integrated.defaultProfile.windows": "PowerShell",
  "terminal.integrated.env.windows": {
    "LANG": "en_US.UTF-8",
    "LC_ALL": "en_US.UTF-8"
  }
}

Recommended Extensions

• C# Dev Kit - C# language support
• PowerShell - Script editing
• Markdown All in One - Documentation preview

Browser Markdown Viewer

For viewing ai/ documentation in a browser:

1. Install Markdown Reader (Chrome/Edge)
2. Click Extensions icon → Markdown Reader → "⋮" → Manage Extension
3. Enable "Allow access to file URLs" (critical - won't work without this)

Resources

• New machine setup: NewMachineBootstrap
• Build environment: HowToBuildSkylineTip
• Claude Code documentation: docs.anthropic.com/claude-code

Feedback

If you discover improvements to the AI-assisted workflow, update the documentation in the ai/ repository. Keeping documentation current helps every developer stay productive.