Nested skill discovery doesn't work for all subdirectories

Description

Skills defined in .claude/skills/ within subdirectories of the working directory are not consistently discovered. In a workspace with two subdirectories at the same level, skills from one subdirectory are discovered but skills from the other are not — even after actively reading and editing files in that subdirectory.

Steps to Reproduce

1. Working directory: C:\Users\user\source\guitar-plugin\
2. Two subdirectories with skills:

• neural-amp-modeler/.claude/skills/ — 3 skills (train-single, train-parametric, create-training-data)
• fictional-octo-happiness/.claude/skills/ — 4 skills (build, commit, release, screenshot)

1. Both have valid SKILL.md files with identical frontmatter format (name, description)
2. Both subdirectories have .claude/settings.local.json files
3. Skills from neural-amp-modeler/ are discovered and usable via /train-single etc.
4. Skills from fictional-octo-happiness/ are never discovered — /build returns "Unknown skill: build"

What I tried

• Actively reading and editing files in fictional-octo-happiness/ during the session
• Checking that SKILL.md frontmatter format matches the working skills exactly
• Verifying directory structure is identical between both subdirectories

Expected Behavior

Per the documentation:

"When you work with files in subdirectories, Claude Code automatically discovers skills from nested .claude/skills/ directories."

Both subdirectories' skills should be discovered.

Environment

• Claude Code CLI on Windows 11
• Both subdirectories are git repositories
• Model: Claude Opus 4.6 (1M context)