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James Russo
ed3ff98ce0
`hyperframes skills update` deleted skills that the same command had just installed, from every agent directory on the machine, and reported them as "no longer published". `skills add --skill '*'` installs every skill in the repo — including the repo-native ones under `.claude/skills/` and `.agents/skills/` — and the upstream lock attributes all of them to `heygen-com/hyperframes`. The published manifest is generated from `<repoRoot>/skills` only (gen-skills-manifest.ts), so it never lists those. detectRemoved read that silence as "removed upstream" and pruned them, so `check || update` could not converge: `add` reinstalled them and the next `update` deleted them again. Scope removed-detection to skills the manifest is actually authoritative for, using the lock's `skillPath` — the only field that separates a skill installed from `skills/` from one installed out of the same repo's other skill roots (`source` is identical for both). An entry with no `skillPath` is treated as not covered: this is a delete path, so unknown provenance fails safe. Also resolve the prune's manifest canonically. Its notion of "still published" could otherwise come from any `skills-manifest.json` within 16 parent directories of cwd, which — since HyperFrames' own manifest declares `source: heygen-com/hyperframes` — matches lock attribution and drives deletion. The install-side check already did this (#2176); the deleting path did not, and the comment claiming that was deliberate and "tested separately" had no such test. An explicit `--source` still wins. Verified end to end against the real CLI in a sandboxed HOME. Before: `add` installed 25 skills, `update` printed "Removing 6 skill(s) no longer published: captions-overlay, changelog-video, cut-the-curve, motion-doctrine, oversized-cursor, seam-craft" and deleted all six (27 dirs -> 21). After: no removal line, 27 -> 27. Both new regression tests fail on the pre-fix source. Fixes #3111