Improve CLI: config store, heartbeat-run, and onboarding

Rework config store with better file handling. Expand heartbeat-run
command with richer output and error reporting. Improve configure
and onboard commands. Update doctor checks.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

cli/src/index.ts

@@ -49,6 +49,7 @@ heartbeat
   )
   .option("--trigger <trigger>", "Trigger detail (manual | ping | callback | system)", "manual")
   .option("--timeout-ms <ms>", "Max time to wait before giving up", "0")
+  .option("--debug", "Show raw adapter stdout/stderr JSON chunks")
   .action(heartbeatRun);
 
 program.parse();