* fix(#4086): resolve skills/ manifest keys at the runtime's actual skills root
Codex installs skills to ~/.agents/skills (skills-kind home override), but
saveLocalPatches() and verify-reapply-patches.cjs resolved every manifest key
config-dir-relative only — every skills/ key missed, so user modifications to
Codex skills were never hash-compared, never backed up, and silently
overwritten on update; the reapply verifier false-failed the same keys with
fail_installed_missing.
configDir stays first (non-override runtimes byte-identical); the skills root
(same _resolveSkillsRootDir / skillsManifestPrefix seams the write side uses)
is a containment-guarded fallback when the config-dir path is absent.
* fix(#4086): drop unused test param; add changeset fragment
* chore(#4086): backfill PR number in changeset fragment
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Co-authored-by: agent-4086 <agent-4086@local>
b327331747