Project-level skills not taking precedence over plugin marketplace skills

Description

When a project-level skill (.claude/skills/) and a plugin marketplace skill (~/.claude/plugins/) provide the same skill name, invoking the skill via the Skill tool loads the plugin version instead of the project-level version. According to the docs, project-level skills should have higher priority than plugin skills.

Steps to Reproduce

1. Install a plugin that provides a skill, e.g., pm-skills marketplace plugin which provides pm-product-discovery:summarize-interview
2. Install a custom version of the same skill at the project level via npx skills add dangrahn/agent-skills, which places it at .claude/skills/pm-product-discovery/skills/summarize-interview/SKILL.md
3. Invoke the skill: /pm-product-discovery:summarize-interview

Expected Behavior

The project-level skill at .claude/skills/pm-product-discovery/skills/summarize-interview/SKILL.md should load, as project-level (priority 3) takes precedence over plugin (priority 4).

Actual Behavior

The plugin version at ~/.claude/plugins/cache/pm-skills/pm-product-discovery/1.0.1/skills/summarize-interview/SKILL.md is loaded instead.

The two versions are significantly different:

• Project-level (custom): Multi-pass analysis workflow with evidence classification, emotional energy mapping, contradictions table, signal strength hierarchy, detailed template with 15+ sections, specific save path
• Plugin (generic): Simple template with 5 fields (Date, Participants, Background, Current Solution, Key Insights, Action Items)

File Locations

# Project-level skill (should win)
.claude/skills/pm-product-discovery/skills/summarize-interview/SKILL.md
.claude/skills/pm-product-discovery/skills/summarize-interview/template.md

# Plugin skill (actually wins)
~/.claude/plugins/cache/pm-skills/pm-product-discovery/1.0.1/skills/summarize-interview/SKILL.md

Possible Cause

The namespaced skill identifier (pm-product-discovery:summarize-interview) may route directly to the plugin without checking for a project-level override first.

Impact

Users who customize skills locally to improve quality, add project-specific save paths, or tailor workflows cannot override generic plugin versions. This defeats the purpose of the precedence system.

Environment

• Claude Code CLI
• macOS (Darwin 24.6.0)
• Skills installed via npx skills add dangrahn/agent-skills
• Plugin installed via marketplace (pm-skills)