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/checks/config-check.ts

@@ -27,7 +27,7 @@ export function configCheck(configPath?: string): CheckResult {
       status: "fail",
       message: `Invalid config: ${err instanceof Error ? err.message : String(err)}`,
       canRepair: false,
-      repairHint: "Run `paperclip onboard` to recreate",
+      repairHint: "Run `paperclip configure --section database` (or `paperclip onboard` to recreate)",
     };
   }
 }