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/runners.ts

@@ -15,7 +15,7 @@ export async function run(_args: string[]): Promise<void> {
   let buildOk = false;
   logger.info('Building agent runners');
   try {
-    execSync('npm run build:runners', {
+    execSync('bun run build:runners', {
       cwd: projectRoot,
       stdio: ['ignore', 'pipe', 'pipe'],
     });