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

.claude/skills/update-skills/SKILL.md

@@ -110,8 +110,8 @@ If a merge fails badly (e.g., cannot resolve conflicts):
 # Step 4: Validation
 
 After all selected skills are merged:
-- `npm run build`
-- `npm test` (do not fail the flow if tests are not configured)
+- `bun run build`
+- `bun test` (do not fail the flow if tests are not configured)
 
 If build fails:
 - Show the error.