ALWAYS load when working on LabKey Server modules (MacCossLabModules, targetedms), in a LabKey enlistment directory, or on GitHub issues/PRs in LabKey repositories.

2026-07-1217

skyline-development

ProteoWizard/pwiz-ai

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

2026-06-1517

night-session

ProteoWizard/pwiz-ai

Invoke when starting an autonomous overnight session ("this is a nighttime autonomous session"). Sets a deep-investigation posture - premium on progress and high-definition findings, expects 5-8 hours of work without check-ins.

2026-06-0517

debugging

ProteoWizard/pwiz-ai

ALWAYS load when investigating bugs, failures, or unexpected behavior - ensures root cause analysis before attempting fixes.

2026-05-1617

name	skyline-wiki
description	Use this skill when reading or updating wiki pages on skyline.ms.

Skyline Wiki Documentation

Full documentation: ai/docs/mcp/wiki.md

When to Read What

Before querying wiki pages: Read ai/docs/mcp/wiki.md (MCP Tools section)
For updating pages: Read ai/docs/mcp/wiki.md (Update Workflow)
For attachments: Read ai/docs/mcp/wiki.md (Attachment section)
For MCP server changes: Read ai/mcp/LabKeyMcp/README.md

Slash Commands

/pw-upconfig - Sync developer config wiki pages with ai/docs source files

Wiki-to-File Mappings

These wiki pages are synced with committed files in the repository:

Wiki Page	Source File	Sync Pattern
AIDevSetup	ai/docs/developer-setup-guide.md	Body (wiki body = file content)
NewMachineBootstrap	ai/docs/new-machine-setup.md	Attachment

Source of truth: The ai/docs files are canonical; wiki pages are updated from them.

Quick Reference

Data location: skyline.ms → /home/software/Skyline → wiki.CurrentWikiVersions

MCP tools available:

list_wiki_pages() - All pages with metadata
get_wiki_page(page_name) - Full content to ai/.tmp/
update_wiki_page(page_name, new_body, title) - Update content
list_wiki_attachments(page_name) - List attached files
get_wiki_attachment(page_name, filename) - Download attachment

Renderer types: HTML, MARKDOWN, RADEOX, TEXT_WITH_LINKS