Root cause: addAutoDiscoveredResources loaded ~/.gsd/agent/skills/
before ~/.agents/skills/, so the legacy directory always won skill
name collisions. After the one-time migration copied skills to
~/.agents/skills/, both directories had identical skills, producing
collision warnings on every boot.
Two fixes:
1. Swap loading order so ~/.agents/skills/ takes precedence
2. Check .migrated-to-agents marker — when present, skip
auto-discovery of the legacy dir entirely (no collisions)
Applied consistently across package-manager, skills.ts,
preferences-skills, and skill-telemetry.
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