feat: register MCP servers via plugin manifest so updates need no setup re-run

[antonbabenko]

Problem

Updating the plugin was a multi-step ritual: /plugin update -> re-run /deliberation:setup -> restart. Root cause: commands/setup.md registered the 5 MCP servers at user scope via claude mcp add, writing a hardcoded absolute versioned cache path into ~/.claude.json:

deliberation-gemini -> node ~/.claude/plugins/cache/antonbabenko/deliberation/<VERSION>/server/gemini/index.js

Every release lands in a new versioned dir, so the path goes stale and only /deliberation:setup rewrites it. Reproduced live: a machine pinned to 3.2.0 while 3.3.0 was already installed in cache.

Fix

Register all 5 servers only in the plugin manifest .claude-plugin/mcp.json (keys deliberation-* / deliberation) with ${CLAUDE_PLUGIN_ROOT} args, which Claude Code re-resolves on every load. The manifest self-heals across versions.

Update flow becomes: /plugin update + /reload-plugins (or restart). No setup re-run, no stale paths.

Tool ids unchanged (zero rules rewrite)

Verified against the Claude Code binary: a plugin manifest server key is used verbatim as the tool namespace, with no plugin-name prefix (mcp__${serverName}__${tool}). So deliberation-codex -> mcp__deliberation-codex__codex. All rules and commands keep working untouched.

Changes

• .claude-plugin/mcp.json - keys renamed to deliberation-* / deliberation; sole runtime MCP registration.
• commands/setup.md - removed the claude mcp add registration + stale-path verification. Now seeds config, installs rules, and one-time removes any stale user-scope deliberation-* entries from a pre-manifest install (migration), then reports status.
• Docs - README.md gains an Updating section (Claude Code flow + non-Claude npx-cache caveat); AGENTS.md / regenerated SKILL.md / POWER.md note the non-Claude update path; CLAUDE.md records the manifest as the sole runtime registration.

Behavior notes

• Per-provider enable/disable continues to gate the unified fan-out (/ask-all, /consensus) via config; the direct provider tools always load (codex is the external codex mcp-server and can't self-gate - accepted).
• Non-Claude hosts unaffected - they register the unified server via npx -y @antonbabenko/deliberation-mcp and never used setup.md or the manifest.

Verification

• npm run check green: typecheck clean, 496 tests pass, 0 fail.
• node scripts/sync-hosts.js run to clear host-artifact drift.
• Namespacing gate confirmed by binary inspection (above).

Not covered in-session (needs a real release cycle)

• The live /plugin update round-trip resolving to the new version with no setup re-run.
• Post-migration cleanup removing stale user-scope entries on a real upgrader's machine.

Out of scope (follow-up)

• Optional in-bridge per-provider gating (so a config-disabled provider's direct tool also hides) - not required for the update fix.
• Pruning the accumulated old cached versions.