fix: remaining npm→pnpm gaps + dockerignore for pnpm symlinks

- container/.dockerignore (new): exclude agent-runner/node_modules and
  agent-runner/dist so COPY agent-runner/ ./ doesn't clobber the
  pnpm-installed node_modules with host directories. Under npm's flat
  layout this was forgiving; under pnpm's symlink layout it's a hard
  conflict (overlay2 cannot copy onto a symlink target).
- setup/{groups,service}.ts: execSync('pnpm run build') not npm.
- setup/index.ts: usage string.
- scripts/*.ts: usage comments + seed-discord final log.
- .claude/settings.json: permission allowlist entries.
- .claude/skills/{add-whatsapp-v2,add-dashboard}/SKILL.md: docs.
- container/skills/{frontend-engineer,vercel-cli,self-customize}/SKILL.md:
  agent-facing docs still told the container agent to run npm.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

scripts/seed-discord.ts

@@ -1,7 +1,7 @@
 /**
  * Seed the v2 central DB with a Discord agent group + messaging group.
  *
- * Usage: npx tsx scripts/seed-discord.ts
+ * Usage: pnpm exec tsx scripts/seed-discord.ts
  */
 import path from 'path';
 
@@ -73,4 +73,4 @@ try {
   }
 }
 
-console.log('Done! Run: npm run build && node dist/index.js');
+console.log('Done! Run: pnpm run build && node dist/index.js');