[BUG] Skills which manually invoke do not automatically invoke

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

I created a series of Claude skills, but one of them—an orchestration skill called "jira-router"—no longer shows up when I ask Claude to list available skills. All my other skills (12 total) appear normally, and jira-router used to work without issues.

Normally, I could say something like "I need to refine OA‑12771", and jira-router would automatically run: it would query JIRA, determine whether the item was a bug, epic, story, etc., and then route the request to the correct skill. That automatic invocation has stopped working. However, manual invocation (e.g., typing /jira-router) still works perfectly, which proves the skill format and content are valid.

Core Issue: This appears to be persistent skill registry corruption tied specifically to the jira-router name/directory. The corruption has survived:

• Multiple Claude Code version upgrades (tested 2.1.7, 2.1.12, 2.1.14, 2.1.15)
• Directory rename jira-router -> `jira-routing'
• Complete removal and reinstallation
• Metadata updates (SKILL.md frontmatter, .dependency-manifest.json, settings.local.json permissions)

Proof it's name-specific corruption:

• Created a brand new skill called jira-router-v2 with identical SKILL.md content → FAILED
• Created a brand new skill called issue-orchestrator with identical SKILL.md content → worked immediately
• This proves the skill content/format is valid and the problem is tied to the corrupted directory/name

Proof it's system-specific:

• Same exact jira-router skill files work perfectly on my laptop (Claude Code 2.1.15)
• Only broken on my desktop system
• This proves it's local state corruption, not a configuration file issue

To troubleshoot, I also tested:

• Running from my user skill path (C:\Users\[username]\.claude\skills\)
• Running from project skill path (.claude\skills\)
• Neither location fixed the issue

Suspected trigger: This problem started after I tested distributing skills to others using custom skill-packager/skill-installer tools. I installed skills to the user path (C:\Users\[username]\.claude\skills\) for testing, then deleted that entire .claude directory (including skills, hooks, settings.json, settings.local.json). It's possible that operation left behind hidden state that permanently corrupted the jira-router skill registry entry on this system.

Attachments:

• claude-code-skill-loading-bug-report.md - Complete technical investigation with evidence
• jira-router-setup-1.9.1-sanitized.zip - The packaged skill for reproduction

jira-router-setup-1.9.1-sanitized.zip
claude-code-skill-loading-bug-report.md

What Should Happen?

When I launch claude it should automatically invoke the jira-router skill when prompts like "i need to refine a JIRA ticket" or "I want to add criteria to an epic" are sent.

Error Messages/Logs

Steps to Reproduce

I am unsure how to replicate, as it seems to be environmental, but Claude and I can't figure out what environmental information would be blocking this skill from loading properly.

Claude Model

Sonnet (default)

Is this a regression?

Yes, this worked in a previous version

Last Working Version

2.1.15

Claude Code Version

2.1.15

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

PowerShell

Additional Information

_No response_