Bug: Skills duplication when 'Agent Skills Location' overlaps with 'Plugin Locations'

Description

When the 'Agent Skills Location' is set to a path that overlaps with 'Plugin Locations', skills are duplicated in the skills list, even though agents are not duplicated. This results in confusion and clutter for users managing skills.

Expected Behavior

Skills should be deduplicated in the UI and internal lists, similar to the deduplication logic applied to agents.

Actual Behavior

Skills appear multiple times if their location matches both 'Agent Skills Location' and 'Plugin Locations'. Agents do not exhibit this duplication.

Steps to Reproduce

1. Set 'Agent Skills Location' to a path that overlaps with 'Plugin Locations'.
2. Observe the skills list: skills are duplicated, but agents are not.

Evidence

See attached screenshots for UI evidence:

• sdd-init command showing skills duplication
• Agent dropdown showing correct deduplication

Environment

• VS Code version: [please fill]
• OS: Linux
• Date: March 16, 2026

Screenshots

Additional context

This deduplication should be applied to skills as it is for agents, to improve usability and avoid confusion.

Please let me know if you need further technical details or reproduction steps.