Custom skill not discovered: ~/.claude/skills/pr-merger/SKILL.md missing from available skills

Bug Description

A custom skill located at ~/.claude/skills/pr-merger/SKILL.md is not being discovered by the skill system. It was working as recently as yesterday (2026-01-30) and stopped appearing in the available skills list today (2026-01-31) without any changes to the file.

Environment

• Claude Code version: Latest (as of 2026-01-31)
• OS: macOS (Darwin 25.2.0, arm64)
• Shell: zsh

Steps to Reproduce

1. Create a skill at ~/.claude/skills/pr-merger/SKILL.md with valid YAML frontmatter:

``yaml
---
name: pr-merger
description: Use when the user wants to shepherd a PR to merge...
allowed-tools: ["Task"]
---
``

1. Start a new Claude Code session
2. Check available skills — pr-merger is missing from the list

Expected Behavior

The skill should appear in the available skills list and be invocable via /pr-merger or automatically triggered by matching phrases.

Actual Behavior

The skill is not listed among available skills. Other skills in the same directory (~/.claude/skills/) ARE discovered correctly:

$ ls ~/.claude/skills/
calculate-coverage     deploy-bcl-packages.md  post-merge-cleanup  pre-pr-review       run-tests
coderabbit-workflow    performance-testing     pr-merger           qodana-local-review  speckit-autopilot.md

Discovered skills (working): run-tests, performance-testing, calculate-coverage, qodana-local-review, post-merge-cleanup, pre-pr-review, coderabbit-workflow, deploy-to-servidor

Not discovered (broken): pr-merger

File Details

• Path: ~/.claude/skills/pr-merger/SKILL.md
• Encoding: UTF-8
• Size: 8967 bytes
• Permissions: -rw-r--r--
• Last modified: 2026-01-30 12:42
• Directory also contains: README.md

Additional Context

• The file has valid YAML frontmatter with name, description, and allowed-tools fields
• No changes were made to the file between when it was working (yesterday) and when it stopped (today)
• All other skills in ~/.claude/skills/ are discovered correctly
• This suggests a regression in skill discovery/loading logic