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The Gemini skills home is the user's own directory. A prior fix only removed a stale entry when it was a symlink into a maintainer-only source, so a deselected skill materialized as a plain directory, or as a symlink into any other source, stayed on disk and still reached the agent. Record the names this lane materializes in a manifest next to the skills, and prune a stale entry only when the manifest names it. An entry the manifest never named — the user's own skill — always survives. The old symlink-into-a-maintainer-only-source check stays as a fallback for a skills home written before this manifest existed. Co-authored-by: Paperclip <noreply@paperclip.ing>