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/index.ts

@@ -1,6 +1,6 @@
 /**
  * Setup CLI entry point.
- * Usage: npx tsx setup/index.ts --step <name> [args...]
+ * Usage: bun setup/index.ts --step <name> [args...]
  */
 import { logger } from '../src/logger.js';
 import { emitStatus } from './status.js';
@@ -23,7 +23,7 @@ async function main(): Promise<void> {
 
   if (stepIdx === -1 || !args[stepIdx + 1]) {
     console.error(
-      `Usage: npx tsx setup/index.ts --step <${Object.keys(STEPS).join('|')}> [args...]`,
+      `Usage: bun setup/index.ts --step <${Object.keys(STEPS).join('|')}> [args...]`,
     );
     process.exit(1);
   }