Get categorized skill set for a manifest

Used by the Credible VS Code extension; not part of the external integration surface. Returns the skills referenced by a manifest, categorized into auto_discovered and supporting groups. malloy-* skills come from the pinned @malloy-publisher/skills npm package; manifests and everything else come from the agent-skills repo. If version is omitted, the server resolves the agent-skills half via the Flagsmith flag agent_skills_version and falls back to the agent_skills_version pin; publisher_skills_version does the same for the npm half. The two halves version independently, so freezing a bundle means naming both. The response reports whichever each half resolved to.