Summary

The collection-based directory reorganization (#643) moved agents, prompts, and instructions from flat directories into {collection}/ subdirectories. However, 34 #file: directives and markdown links across 15 files were not updated to reflect the new directory depth. All broken references follow the same pattern: they use one ../ traversal when two are now required, and they omit the collection subdirectory name.

Root Cause

Before the reorg, files were structured as:

.github/prompts/github-triage-issues.prompt.md
.github/instructions/github-backlog-triage.instructions.md

A reference #file:../instructions/github-backlog-triage.instructions.md from a prompt correctly resolved to .github/instructions/github-backlog-triage.instructions.md.

After the reorg:

.github/prompts/github/github-triage-issues.prompt.md
.github/instructions/github/github-backlog-triage.instructions.md

The same reference #file:../instructions/github-backlog-triage.instructions.md now resolves to .github/prompts/instructions/github-backlog-triage.instructions.md, which does not exist.

Fix Pattern

#file:../instructions/{filename}.md → #file:../../instructions/{collection}/{filename}.md
[text](../instructions/{filename}.md) → [text](../../instructions/{collection}/{filename}.md)

Broken References

ADO Collection (7 references in 2 files)

GitHub Collection (19 references in 6 files)

HVE-Core Collection (3 references in 3 files)

Acceptance Criteria

• All 34 broken #file: directives and markdown links are updated with correct paths
• npm run lint:all passes
• npm run plugin:generate succeeds
• Manual verification that #file: directives resolve in VS Code after the fix

Related Issues

• feat: Reorganize agents, instructions, prompts, and skills into collection-based subdirectories #643 — Reorganize artifacts into collection-based subdirectories (the reorg that caused these breaks)
• fix: AI generated .copilot-tracking files produce broken relative paths flooding VS Code Problems tab #698 — Generated .copilot-tracking files produce broken relative paths (related path portability)