Custom skills no longer working after new installation caused a name collision between bundled skill and custom skill

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?

Bug Report: Custom Skills Stopped Working in VSCode Extension

Problem

Custom skills in ~/.claude/skills/ stopped working after upgrading from v2.1.177 → v2.1.179. All slash commands return "Unknown command" and skills don't appear in the available skills list.

Root Cause Hypothesis

When v2.1.178 introduced the bundled code-review skill, it created a name conflict with my custom code-review.md skill, which corrupted the skill loading system for ALL custom skills. The corruption persists even after renaming/removing the conflicting skill and downgrading.

What Worked Yesterday (v2.1.177)

• Custom /code-review skill with CLI arguments worked via slash commands
• All custom skills in ~/.claude/skills/*.md were invocable

What's Broken Now

• All custom skills fail to load (not in available skills list)
• Slash commands: "Unknown command: /skill-name"
• Skill tool: "Unknown skill: skill-name"
• Bundled skills (/code-review, /simplify) work fine

Troubleshooting Attempts (4+ hours)

• Tested 50+ versions (v2.1.128 → v2.1.170) - custom skills don't work in any
• Renamed conflicting skill: code-review.md → ndex-code-review.md - no effect
• Cleared all caches: ~/.claude/.claude.json, ~/.claude/plugins/*
• Tried plugin structure with .claude-plugin/manifest.json - didn't help
• Created minimal test skill (hello-kelly.md) - doesn't load
• Emptied skills directory completely - no change
• Reset ~/.claude/settings.json to defaults
• Multiple full VSCode restarts

Test Case

Simple skill that fails to load:

~/.claude/skills/hello-kelly.md:

---
name: hello-kelly
user_invocable: true
description: Simple test skill
---
Output: **Hello Kelly!**

Result: /hello-kelly returns "Unknown command"

Environment

• Platform: Linux (Amazon Linux 2023), VSCode Remote SSH
• Extension versions tested: v2.1.128, v2.1.152, v2.1.159, v2.1.169, v2.1.170, v2.1.178, v2.1.179
• Affected custom skills (backed up to ~/kelly-claude-skills/): code-review, jira-export, jira-create-feature, inspector-analyze, inspector-morning-scan

Expected Fix

Custom skills should auto-load from ~/.claude/skills/*.md without conflicts from bundled skills.

---
Contact: kpeterman2@ndex.gov | Date: 2026-06-17

What Should Happen?

I would expect my custom skills that worked yesterday to continue to work. And that the custom code-review skill I created will work after I have renamed it.

Error Messages/Logs

Steps to Reproduce

1. Create a skill and use that skill that has the same name as a skill that is installed on top of custom skill
2. New Claude Code vscode plugin is auto installed on vscode start up
3. Notice that when typing /code-review a completely different behavior starts.
4. Attempt to rename custom code-review skill to blah-code-review. renamed custom skill doesn't work
5. Test other custom skills that used to work like backlog grooming and aws inspector export and analysis. None of previous custom skills work
6. Create new custom skill that is basically a hello world. Again does not work

It appears like all custom skills no longer register.

Claude Model

Sonnet (default)

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

2.1.179

Platform

AWS Bedrock

Operating System

Windows

Terminal/Shell

VS Code integrated terminal

Additional Information

_No response_