skyline-development

name	skyline-development
description	ALWAYS load when working in pwiz_tools/Skyline, on GitHub issues labeled 'skyline', or TODOs referencing Skyline code.

Skyline Development Context

When working on any Skyline/ProteoWizard task, consult these documentation files for essential context.

Starting Work on a TODO

When starting a new TODO or sprint, read ai/todos/STARTUP.md first. It provides:

• Essential context files to read (CRITICAL-RULES.md, MEMORY.md, WORKFLOW.md)
• Git branch workflow (create from master, copy TODO to active/)
• TODO lifecycle (backlog → active → completed)

Continuing Work on Current Branch

When asked to continue work on the current branch or its TODO:

1. Call mcp__status__get_project_status() to get branch name (e.g., Skyline/work/20251126_files_view)
2. Extract date and feature name from branch (e.g., 20251126_files_view)
3. Read the TODO file at ai/todos/active/TODO-{date}_{feature}.md
4. The TODO contains: objective, PR link, completed tasks, remaining work, and context

Core Files (Read for Every Code Task)

Read these files to understand project constraints and patterns:

1. ai/CRITICAL-RULES.md - Absolute constraints (NO async/await, resource strings only, CRLF line endings, naming conventions)
2. ai/MEMORY.md - Project context (900K LOC, 17 years, 8 devs, critical gotchas)
3. ai/WORKFLOW.md - Git workflows, TODO system, commit message format
4. ai/STYLEGUIDE.md - C# coding conventions for Skyline
5. ai/TESTING.md - Testing rules (translation-proof, test structure)

When to Read What

• Before writing code: Read CRITICAL-RULES.md, STYLEGUIDE.md
• Before writing tests: Read TESTING.md, ai/docs/testing-patterns.md
• Before committing: Read WORKFLOW.md (commit message rules, Co-Authored-By attribution)
• Before building/testing: Read ai/docs/build-and-test-guide.md
• For detailed patterns: Read files in ai/docs/

Key Constraints (Quick Reference)

• NO async/await - Use ActionUtil.RunAsync() instead
• ALL user-facing text in .resx files - No string literals
• NEVER English text in test assertions - Use resource strings
• Line endings: CRLF - Windows standard
• Private fields: _camelCase - Not m_ prefix
• Always include Co-Authored-By: Claude <[e-mail]> in commits
• CLI args must work via MCP RunCommand() - Every SkylineCmd argument is also driven by an LLM through the in-process Skyline MCP, which saves via the GUI path (SkylineFiles.SaveDocument), not CommandLine's. Don't thread per-invocation state through the SaveDocument/Serialize* signatures (the MCP path drops it); use a scoped ambient override set in CommandLine.RunInner and read at the convergence point all save paths share (DocumentWriter → CompactFormatOption.Effective). See PR #4288.

Slash Commands Available

Type /pw- to see all project-specific commands. Key ones:

• /pw-context - Full context reload
• /pw-rcrw - Review critical rules and workflow
• /pw-pcommitfull - Pre-commit with TODO update
• /pw-help - Full command reference