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`hyperframes init` / `skills` / `skills update` shelled out to `skills add` without `--copy`, so the upstream CLI installed via its canonical `.agents/skills` store + per-agent symlinks. That layout re-serialises each SKILL.md's frontmatter, so an installed bundle no longer byte-matches the published manifest — `skills check` reported a freshly-installed set as outdated — and it didn't reliably land in the dir the agent reads (e.g. `.claude/skills`). Pass `--copy` in runSkillsAdd (the single chokepoint every install flows through: bare `skills`, `update`, and `init` via installAllSkills) so real files are written into each agent's skills dir — faithful to the manifest and correctly placed. Verified end-to-end: a fresh-content install now reads all-current in `.claude/skills` (was all-outdated in `agent/skills`). Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>