Custom skill loaded and invocable via / but not included in system-reminder skill listing

Environment: Claude Code v2.1.37, macOS Darwin 25.2.0

Problem: A custom skill (pr-merger) in ~/.claude/skills/pr-merger/SKILL.md with valid YAML frontmatter is loaded by Claude Code (appears in / autocomplete, can be invoked), but is NOT included in the system-reminder's skill listing. This means Claude cannot see or proactively use the skill.

Expected behavior: All valid skills in ~/.claude/skills/ should appear in the system-reminder skill listing.

Reproduction steps:

1. Have 7 custom skills in ~/.claude/skills/ (all symlinked directories with SKILL.md + YAML frontmatter)
2. Start a new session: claude --permission-mode plan
3. Type /pr — autocomplete shows /pr-merger - PR Merger Skill (user)
4. Ask Claude "What skills are in system-reminder's skill list?" — pr-merger is missing
5. Ask Claude to "use pr-merger skill" — Claude says "There is no pr-merger skill available"

Investigation: Verified SKILL.md encoding (UTF-8, LF), permissions (-rw-r--r--), frontmatter format (identical to working skills), symlink resolution (valid). No obvious difference between working and non-working skills.

Working skills: coderabbit-workflow, performance-testing, post-merge-cleanup, pre-pr-review (all symlinked Jan 18)

Non-working skill: pr-merger (symlinked Feb 8, same source repo, same structure)