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/init-first-agent.ts

@@ -10,7 +10,7 @@
  * channel adapters, so there's no Gateway conflict.
  *
  * Usage:
- *   npx tsx scripts/init-first-agent.ts \
+ *   pnpm exec tsx scripts/init-first-agent.ts \
  *     --channel discord \
  *     --user-id discord:1470183333427675709 \
  *     --platform-id discord:@me:1491573333382523708 \

scripts/migrate-group-claude-md.ts

@@ -22,7 +22,7 @@
  *
  * Idempotent — safe to re-run.
  *
- * Usage: npx tsx scripts/migrate-group-claude-md.ts
+ * Usage: pnpm exec tsx scripts/migrate-group-claude-md.ts
  */
 import fs from 'fs';
 import path from 'path';

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');

scripts/test-v2-agent.ts

@@ -2,7 +2,7 @@
  * Quick integration test: create a session DB, insert a message,
  * run the v2 poll loop with the Claude provider, verify output.
  *
- * Usage: npx tsx scripts/test-v2-agent.ts
+ * Usage: pnpm exec tsx scripts/test-v2-agent.ts
  */
 import Database from 'better-sqlite3';
 import fs from 'fs';

scripts/test-v2-channel-e2e.ts

@@ -4,7 +4,7 @@
  * Mock adapter → onInbound → router → session DB → Docker container →
  * agent-runner → Claude → messages_out → delivery → mock adapter.deliver()
  *
- * Usage: npx tsx scripts/test-v2-channel-e2e.ts
+ * Usage: pnpm exec tsx scripts/test-v2-channel-e2e.ts
  */
 import Database from 'better-sqlite3';
 import fs from 'fs';

scripts/test-v2-host.ts

@@ -6,7 +6,7 @@
  * 3. Container runs v2 agent-runner, polls inbound.db, queries Claude, writes outbound.db
  * 4. Poll outbound.db for messages_out response
  *
- * Usage: npx tsx scripts/test-v2-host.ts
+ * Usage: pnpm exec tsx scripts/test-v2-host.ts
  */
 import Database from 'better-sqlite3';
 import fs from 'fs';