chore: replace all node/npm/tsx references with bun across codebase

- Source: setup/service.ts, runners.ts, agent-runner.ts error messages
- Scripts: restart-stack.sh, run-migrations.ts → bun
- Bootstrap: setup.sh check_node→check_bun, npm install→bun install
- Docs: CLAUDE.md, README.md, all SKILL.md files
- Tests: service.test.ts, restart-stack.test.ts expectations updated

setup/restart-stack.test.ts

@@ -155,7 +155,7 @@ describe('restartStackServices', () => {
         serviceManager: 'systemd',
         serviceId: 'codex-main',
       }),
-    ).toThrow('Run `npm run setup -- --step service`');
+    ).toThrow('Run `bun run setup -- --step service`');
   });
 
   it('does not hide a general start failure behind direct fallback', () => {